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  1. The ability to genetically manipulate bacteria has been fundamentally important for both basic biological discovery and translational research to develop new vaccines and antibiotics. Experimental alteration o...

    Authors: Sebastián Aguilar Pierlé, Gena Kenitra Hammac, Guy H Palmer and Kelly A Brayton
    Citation: BMC Genomics 2013 14:272
    Content type: Research article Published on:

  2. Wheat yellow (stripe) rust caused by Puccinia striiformis f. sp. tritici (PST) is one of the most devastating diseases of wheat worldwide. To design effective breeding strategies that maximize the potential for d...

    Authors: Dario Cantu, Vanesa Segovia, Daniel MacLean, Rosemary Bayles, Xianming Chen, Sophien Kamoun, Jorge Dubcovsky, Diane GO Saunders and Cristobal Uauy
    Citation: BMC Genomics 2013 14:270
    Content type: Research article Published on:

  5. The ability of the human malarial parasite Plasmodium falciparum to invade, colonise and multiply within diverse host environments, as well as to manifest its virulence within the human host, are activities tight...

    Authors: Karen Russell, Sandra Hasenkamp, Richard Emes and Paul Horrocks
    Citation: BMC Genomics 2013 14:267
    Content type: Research article Published on:

  6. Nematostella vectensis, a burrowing sea anemone, has become a popular species for the study of cnidarian development. In previous studies, the expression of a variety of genes has been characterized during N. vec...

    Authors: Rebecca Rae Helm, Stefan Siebert, Sarah Tulin, Joel Smith and Casey William Dunn
    Citation: BMC Genomics 2013 14:266
    Content type: Research article Published on:

  7. miRNA profiling performed in myogenic cells and biopsies from skeletal muscles has previously identified miRNAs involved in myogenesis.

    Authors: Petr Dmitriev, Ana Barat, Anna Polesskaya, Mary J O’Connell, Thomas Robert, Philippe Dessen, Thomas A Walsh, Vladimir Lazar, Ahmed Turki, Gilles Carnac, Dalila Laoudj-Chenivesse, Marc Lipinski and Yegor S Vassetzky
    Citation: BMC Genomics 2013 14:265
    Content type: Methodology article Published on:

  8. Validation of physiologic miRNA targets has been met with significant challenges. We employed HITS-CLIP to identify which miRNAs participate in liver regeneration, and to identify their target mRNAs.

    Authors: Jonathan Schug, Lindsay B McKenna, Gabriel Walton, Nicholas Hand, Sarmistha Mukherjee, Kow Essuman, Zhongjie Shi, Yan Gao, Karen Markley, Momo Nakagawa, Vasumathi Kameswaran, Anastassios Vourekas, Joshua R Friedman, Klaus H Kaestner and Linda E Greenbaum
    Citation: BMC Genomics 2013 14:264
    Content type: Research article Published on:

  9. The Chinese pine (Pinus tabuliformis) is an indigenous conifer species in northern China but is relatively underdeveloped as a genomic resource; thus, limiting gene discovery and breeding. Large-scale transcripto...

    Authors: Shi-Hui Niu, Zhe-Xin Li, Hu-Wei Yuan, Xiao-Yang Chen, Yue Li and Wei Li
    Citation: BMC Genomics 2013 14:263
    Content type: Research article Published on:

  10. Copy number variants contribute to genetic variation in birds. Analyses of copy number variants in chicken breeds had focused primarily on those from commercial varieties with nothing known about the occurrenc...

    Authors: Ming Tian, Yanqiang Wang, Xiaorong Gu, Chungang Feng, Suyun Fang, Xiaoxiang Hu and Ning Li
    Citation: BMC Genomics 2013 14:262
    Content type: Research article Published on:

  11. There is increasing evidence of the importance of copy number variants (CNV) in genetic diversity among individuals and populations, as well as in some common genetic diseases. We previously characterized a co...

    Authors: Laia Bassaganyas, Eva Riveira-Muñoz, Manel García-Aragonés, Juan R González, Mario Cáceres, Lluís Armengol and Xavier Estivill
    Citation: BMC Genomics 2013 14:261
    Content type: Research article Published on:

  12. After publication of this article (Fernandez et al., BMC Genomics 2011, 12:604) it was brought to the Editors’ attention that the data generated by the first author, Ariel Fernandez, seemed anomalous. One of the ...

    Authors: Maria K Kowalczuk, Shreeya Nanda and Elizabeth C Moylan
    Citation: BMC Genomics 2013 14:260
    Content type: Erratum Published on:

    The original article was published in BMC Genomics 2011 12:604

  13. Environmental temperature directly affects the concentrations of chemicals in the gas phase. Therefore, if the olfactory system does not physiologically adapt to environmental conditions, it may provide inadeq...

    Authors: Jacob Riveron, Tamara Boto and Esther Alcorta
    Citation: BMC Genomics 2013 14:259
    Content type: Research article Published on:

  14. Overexpression of the Cut homeobox 1 gene, CUX1, inverselycorrelates with patient survival in breast cancers. Cell-based assays andmolecular studies have revealed that transcriptional regulation byCUX1 involves m...

    Authors: Charles Vadnais, Arif A Awan, Ryoko Harada, Pier-Luc Clermont, Lam Leduy, Ginette Bérubé and Alain Nepveu
    Citation: BMC Genomics 2013 14:258
    Content type: Research article Published on:

  15. Paired-tag sequencing approaches are commonly used for the analysis of genome structure. However, mammalian genomes have a complex organization with a variety of repetitive elements that complicate comprehensi...

    Authors: Sebastiaan van Heesch, Wigard P Kloosterman, Nico Lansu, Frans-Paul Ruzius, Elizabeth Levandowsky, Clarence C Lee, Shiguo Zhou, Steve Goldstein, David C Schwartz, Timothy T Harkins, Victor Guryev and Edwin Cuppen
    Citation: BMC Genomics 2013 14:257
    Content type: Research article Published on:

  16. The transmission of the malaria parasite Plasmodium falciparum from the human to the mosquito is mediated by dormant sexual precursor cells, the gametocytes, which become activated in the mosquito midgut. Because...

    Authors: Che Julius Ngwa, Matthias Scheuermayer, Gunnar Rudolf Mair, Selina Kern, Thomas Brügl, Christine Clara Wirth, Makoah Nigel Aminake, Jochen Wiesner, Rainer Fischer, Andreas Vilcinskas and Gabriele Pradel
    Citation: BMC Genomics 2013 14:256
    Content type: Research article Published on:

  17. Staphylococcus epidermidis bacteria are a major cause of biomaterial-associated infections in modern medicine. Yet there is little known about the host responses against this normally innocent bacterium in the co...

    Authors: Wouter J Veneman, Oliver W Stockhammer, Leonie de Boer, Sebastian A J Zaat, Annemarie H Meijer and Herman P Spaink
    Citation: BMC Genomics 2013 14:255
    Content type: Research article Published on:

  19. Targeted capture, combined with massively-parallel sequencing, is a powerful technique that allows investigation of specific portions of the genome for less cost than whole genome sequencing. Several methods h...

    Authors: Jamie K Teer, Jennifer J Johnston, Sarah L Anzick, Marbin Pineda, Gary Stone, Paul S Meltzer, James C Mullikin and Leslie G Biesecker
    Citation: BMC Genomics 2013 14:253
    Content type: Methodology article Published on:

  20. During host specialization, inactivation of genes whose function is no more required is favored by changes in selective constraints and evolutionary bottlenecks. The Gram positive bacteria Streptococcus agalactia...

    Authors: Isabelle Rosinski-Chupin, Elisabeth Sauvage, Barbara Mairey, Sophie Mangenot, Laurence Ma, Violette Da Cunha, Christophe Rusniok, Christiane Bouchier, Valérie Barbe and Philippe Glaser
    Citation: BMC Genomics 2013 14:252
    Content type: Research article Published on:

  21. Efficient mechanisms for rejoining of DNA double-strand breaks (DSBs) are vital because misrepair of such lesions leads to mutation, aneuploidy and loss of cell viability. DSB repair is mediated by proteins ac...

    Authors: Jennifer Summers McKinney, Sunaina Sethi, Jennifer DeMars Tripp, Thuy N Nguyen, Brian A Sanderson, James W Westmoreland, Michael A Resnick and L Kevin Lewis
    Citation: BMC Genomics 2013 14:251
    Content type: Research article Published on:

  22. The Brassica B genome is known to carry several important traits, yet there has been limited analyses of its underlying genome structure, especially in comparison to the closely related A and C genomes. A bacteri...

    Authors: Zahra-Katy Navabi, Terry Huebert, Andrew G Sharpe, Carmel M O’Neill, Ian Bancroft and Isobel AP Parkin
    Citation: BMC Genomics 2013 14:250
    Content type: Research article Published on:

  23. Sequence-specific DNA-binding proteins, with their paramount importance in the regulation of expression of the genetic material, are encoded by approximately 5% of the genes in an animal’s genome. But it is un...

    Authors: Hannah L Craig, Julia Wirtz, Sophie Bamps, Colin T Dolphin and Ian A Hope
    Citation: BMC Genomics 2013 14:249
    Content type: Research article Published on:

  24. Senescence-accelerated mice (SAM) are a series of mouse strains originally derived from unexpected crosses between AKR/J and unknown mice, from which phenotypically distinct senescence-prone (SAMP) and -resist...

    Authors: Kumpei Tanisawa, Eri Mikami, Noriyuki Fuku, Yoko Honda, Shuji Honda, Ikuro Ohsawa, Masafumi Ito, Shogo Endo, Kunio Ihara, Kinji Ohno, Yuki Kishimoto, Akihito Ishigami, Naoki Maruyama, Motoji Sawabe, Hiroyoshi Iseki, Yasushi Okazaki…
    Citation: BMC Genomics 2013 14:248
    Content type: Research article Published on:

  25. Citrus huanglongbing (HLB) disease is caused by endogenous, phloem-restricted, Gram negative, uncultured bacteria named Candidatus Liberibacter africanus (CaLaf), Ca. L. asiaticus (CaLas), and Ca. L. americanus (...

    Authors: Valéria Mafra, Polyana K Martins, Carolina S Francisco, Marcelo Ribeiro-Alves, Juliana Freitas-Astúa and Marcos A Machado
    Citation: BMC Genomics 2013 14:247
    Content type: Research article Published on:

  26. Recent studies had found thousands of natural antisense transcripts originating from the same genomic loci of protein coding genes but from the opposite strand. It is unclear whether the majority of antisense ...

    Authors: Maurice HT Ling, Yuguang Ban, Hongxiu Wen, San Ming Wang and Steven X Ge
    Citation: BMC Genomics 2013 14:243
    Content type: Research article Published on:

  27. Genome-wide analysis was performed to assess the transcriptional landscape of germinating A. niger conidia using both next generation RNA-sequencing and GeneChips. The metabolism of storage compounds during conid...

    Authors: Michaela Novodvorska, Kimran Hayer, Steven T Pullan, Raymond Wilson, Martin J Blythe, Hein Stam, Malcolm Stratford and David B Archer
    Citation: BMC Genomics 2013 14:246
    Content type: Research article Published on:

  28. Panax ginseng C. A. Meyer is one of the most widely used medicinal plants. Complete genome information for this species remains unavailable due to its large genome size. At present, analysis of expressed sequence...

    Authors: Chunfang Li, Yingjie Zhu, Xu Guo, Chao Sun, Hongmei Luo, Jingyuan Song, Ying Li, Lizhi Wang, Jun Qian and Shilin Chen
    Citation: BMC Genomics 2013 14:245
    Content type: Research article Published on:

  29. The Setaria genus is increasingly of interest to researchers, as its two species, S. viridis and S. italica, are being developed as models for understanding C4 photosynthesis and plant functional genomics. The ge...

    Authors: Meicheng Zhao, Hui Zhi, Andrew N Doust, Wei Li, Yongfang Wang, Haiquan Li, Guanqing Jia, Yongqiang Wang, Ning Zhang and Xianmin Diao
    Citation: BMC Genomics 2013 14:244
    Content type: Research article Published on:

  30. Streptococcus pneumoniae causes over one million deaths worldwide annually, despite recent developments in vaccine and antibiotic therapy. Host susceptibility to pneumococcal infection and disease is controlled b...

    Authors: Laura Wisby, Vitor E Fernandes, Daniel R Neill, Aras Kadioglu, Peter W Andrew and Paul Denny
    Citation: BMC Genomics 2013 14:242
    Content type: Research article Published on:

  31. Cotton (Gossypium hirsutum L.) is a major fiber crop that is grown worldwide; it faces extensive damage from sap-sucking insects, including aphids and whiteflies. Genome-wide transcriptome analysis was performed ...

    Authors: Neeraj Kumar Dubey, Ridhi Goel, Alok Ranjan, Asif Idris, Sunil Kumar Singh, Sumit K Bag, Krishnappa Chandrashekar, Kapil Deo Pandey, Pradhyumna Kumar Singh and Samir V Sawant
    Citation: BMC Genomics 2013 14:241
    Content type: Research article Published on:

  32. The recA/RAD51 gene family encodes a diverse set of recombinase proteins that affect homologous recombination, DNA-repair, and genome stability. The recA gene family is expressed across all three domains of li...

    Authors: Sree V Chintapalli, Gaurav Bhardwaj, Jagadish Babu, Loukia Hadjiyianni, Yoojin Hong, George K Todd, Casey A Boosalis, Zhenhai Zhang, Xiaofan Zhou, Hong Ma, Andriy Anishkin, Damian B van Rossum and Randen L Patterson
    Citation: BMC Genomics 2013 14:240
    Content type: Research article Published on:

  33. The gene doublesex (dsx) is known as a key factor regulating genetic sex determination in many organisms. We previously identified two dsx genes (DapmaDsx1 and DapmaDsx2) from a freshwater branchiopod crustacean,...

    Authors: Kenji Toyota, Yasuhiko Kato, Masaru Sato, Naomi Sugiura, Shinichi Miyagawa, Hitoshi Miyakawa, Hajime Watanabe, Shigeto Oda, Yukiko Ogino, Chizue Hiruta, Takeshi Mizutani, Norihisa Tatarazako, Susanne Paland, Craig Jackson, John K Colbourne and Taisen Iguchi
    Citation: BMC Genomics 2013 14:239
    Content type: Research article Published on:

  34. Nicotianamine (NA), a ubiquitous molecule in plants, is an important metal ion chelator and the main precursor for phytosiderophores biosynthesis. Considerable progress has been achieved in cloning and charact...

    Authors: Xiaojin Zhou, Suzhen Li, Qianqian Zhao, Xiaoqing Liu, Shaojun Zhang, Cheng Sun, Yunliu Fan, Chunyi Zhang and Rumei Chen
    Citation: BMC Genomics 2013 14:238
    Content type: Research article Published on:

  35. Whole transcriptome analyses are an essential tool for understanding disease mechanisms. Approaches based on next-generation sequencing provide fast and affordable data but rely on the availability of annotate...

    Authors: Roland Schmucki, Marco Berrera, Erich Küng, Serene Lee, Wolfgang E Thasler, Sabine Grüner, Martin Ebeling and Ulrich Certa
    Citation: BMC Genomics 2013 14:237
    Content type: Methodology article Published on:

  36. In temperate regions, the time lag between vegetative bud burst and bud set determines the duration of the growing season of trees (i.e. the duration of wood biomass production). Dormancy, the period during wh...

    Authors: Saneyoshi Ueno, Christophe Klopp, Jean Charles Leplé, Jérémy Derory, Céline Noirot, Valérie Léger, Elodie Prince, Antoine Kremer, Christophe Plomion and Grégoire Le Provost
    Citation: BMC Genomics 2013 14:236
    Content type: Research article Published on:

  37. Nutritional symbioses play a central role in insects’ adaptation to specialized diets and in their evolutionary success. The obligatory symbiosis between the pea aphid, Acyrthosiphon pisum, and the bacterium, Buc...

    Authors: Andréane Rabatel, Gérard Febvay, Karen Gaget, Gabrielle Duport, Patrice Baa-Puyoulet, Panagiotis Sapountzis, Nadia Bendridi, Marjolaine Rey, Yvan Rahbé, Hubert Charles, Federica Calevro and Stefano Colella
    Citation: BMC Genomics 2013 14:235
    Content type: Research article Published on:

  38. Understanding the processes that drive the evolution of snake venom is a topic of great research interest in molecular and evolutionary toxinology. Recent studies suggest that ontogenetic changes in venom comp...

    Authors: Jordi Durban, Alicia Pérez, Libia Sanz, Aarón Gómez, Fabián Bonilla, Santos Rodríguez, Danilo Chacón, Mahmood Sasa, Yamileth Angulo, José M Gutiérrez and Juan J Calvete
    Citation: BMC Genomics 2013 14:234
    Content type: Research article Published on:

  39. MicroRNAs (miRNAs) are endogenous small RNAs (sRNAs) with a wide range of regulatory functions in plant development and stress responses. Although miRNAs associated with plant drought stress tolerance have bee...

    Authors: Peng Shuai, Dan Liang, Zhoujia Zhang, Weilun Yin and Xinli Xia
    Citation: BMC Genomics 2013 14:233
    Content type: Research article Published on:

  40. The Estrogen Receptor alpha (ERα) is the key transcriptional regulator in luminal breast cancer and is therefore the main target for adjuvant treatment of this subtype. Luminal gene signatures are dictated by ...

    Authors: Wilbert Zwart, Rutger Koornstra, Jelle Wesseling, Emiel Rutgers, Sabine Linn and Jason S Carroll
    Citation: BMC Genomics 2013 14:232
    Content type: Methodology article Published on:

  41. Mycobacterium bovis, the causative agent of bovine tuberculosis, is an intracellular pathogen that can persist inside host macrophages during infection via a diverse range of mechanisms that subvert the host immu...

    Authors: Nicolas C Nalpas, Stephen DE Park, David A Magee, Maria Taraktsoglou, John A Browne, Kevin M Conlon, Kévin Rue-Albrecht, Kate E Killick, Karsten Hokamp, Amanda J Lohan, Brendan J Loftus, Eamonn Gormley, Stephen V Gordon and David E MacHugh
    Citation: BMC Genomics 2013 14:230
    Content type: Research article Published on:

  42. In recent years, genome-wide association studies have successfully uncovered single-nucleotide polymorphisms (SNPs) associated with complex traits such as diseases and quantitative phenotypes. These variations...

    Authors: Jiasen Liu, Li Zhang, Lingyang Xu, Hangxing Ren, Jian Lu, Xiaoning Zhang, Shifang Zhang, Xinlei Zhou, Caihong Wei, Fuping Zhao and Lixin Du
    Citation: BMC Genomics 2013 14:229
    Content type: Research article Published on:

  43. Ecosystems worldwide are suffering the consequences of anthropogenic impact. The diverse ecosystem of coral reefs, for example, are globally threatened by increases in sea surface temperatures due to global wa...

    Authors: Camila Granados-Cifuentes, Anthony J Bellantuono, Tyrone Ridgway, Ove Hoegh-Guldberg and Mauricio Rodriguez-Lanetty
    Citation: BMC Genomics 2013 14:228
    Content type: Research article Published on:

  44. Agarwood is an expensive resinous heartwood derived from Aquilaria plants that is widely used in traditional medicines, incense and perfume. Only wounded trees can produce agarwood, and the huge demand for the ag...

    Authors: Yanhong Xu, Zheng Zhang, Mengxi Wang, Jianhe Wei, Hongjiang Chen, Zhihui Gao, Chun Sui, Hongmei Luo, Xingli Zhang, Yun Yang, Hui Meng and Wenlan Li
    Citation: BMC Genomics 2013 14:227
    Content type: Research article Published on:

  45. In all Metazoa, transcription is inactive during the first mitotic cycles after fertilisation. In Drosophila melanogaster, Zygotic Genome Activation (ZGA) occurs in two waves, starting respectively at mitotic cyc...

    Authors: Elodie Darbo, Carl Herrmann, Thomas Lecuit, Denis Thieffry and Jacques van Helden
    Citation: BMC Genomics 2013 14:226
    Content type: Research article Published on:

  46. Horizontal gene transfer has shaped the evolution of the ammonium transporter/ammonia permease gene family. Horizontal transfers of ammonium transporter/ammonia permease genes into the fungi include one transf...

    Authors: Tami R McDonald, Olaf Mueller, Fred S Dietrich and François Lutzoni
    Citation: BMC Genomics 2013 14:225
    Content type: Research article Published on:

  47. Cellular senescence can be induced by a variety of extrinsic stimuli, and sustained exposure to sunlight is a key factor in photoaging of the skin. Accordingly, irradiation of skin fibroblasts by UVB light tri...

    Authors: Ruth Greussing, Matthias Hackl, Pornpimol Charoentong, Alexander Pauck, Rossella Monteforte, Maria Cavinato, Edith Hofer, Marcel Scheideler, Michael Neuhaus, Lucia Micutkova, Christoph Mueck, Zlatko Trajanoski, Johannes Grillari and Pidder Jansen-Dürr
    Citation: BMC Genomics 2013 14:224
    Content type: Research article Published on:

  48. Although the genome sequence of the protozoan parasite Leishmania major was determined several years ago, the knowledge of its transcriptome was incomplete, both regarding the real number of genes and their prima...

    Authors: Alberto Rastrojo, Fernando Carrasco-Ramiro, Diana Martín, Antonio Crespillo, Rosa M Reguera, Begoña Aguado and Jose M Requena
    Citation: BMC Genomics 2013 14:223
    Content type: Research article Published on:

  49. The assembly of the bread wheat genome sequence is challenging due to allohexaploidy and extreme repeat content (>80%). Isolation of single chromosome arms by flow sorting can be used to overcome the polyploid...

    Authors: Tatiana Belova, Bujie Zhan, Jonathan Wright, Mario Caccamo, Torben Asp, Hana Šimková, Matthew Kent, Christian Bendixen, Frank Panitz, Sigbjørn Lien, Jaroslav Doležel, Odd-Arne Olsen and Simen R Sandve
    Citation: BMC Genomics 2013 14:222
    Content type: Research article Published on:

  50. Human leukocyte antigen matching at allelic resolution is proven clinically significant in hematopoietic stem cell transplantation, lowering the risk of graft-versus-host disease and mortality. However, due to...

    Authors: Martin Danzer, Norbert Niklas, Stephanie Stabentheiner, Katja Hofer, Johannes Pröll, Christina Stückler, Edeltraud Raml, Helene Polin and Christian Gabriel
    Citation: BMC Genomics 2013 14:221
    Content type: Methodology article Published on:

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BMC Genomics

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