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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  5. 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:

  6. 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:

  7. 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:

  8. 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:

  9. 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:

  10. 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:

  11. 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:

  12. 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:

  13. 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:

  14. 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:

  15. 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:

  16. 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:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  21. 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:

  22. The availability of gene expression data that corresponds to pig immune response challenges provides compelling material for the understanding of the host immune system. Meta-analysis offers the opportunity to...

    Authors: Bouabid Badaoui, Christopher K Tuggle, Zhiliang Hu, James M Reecy, Tahar Ait-Ali, Anna Anselmo and Sara Botti
    Citation: BMC Genomics 2013 14:220
    Content type: Research article Published on:

  23. Olive cDNA libraries to isolate candidate genes that can help enlightening the molecular mechanism of periodicity and / or fruit production were constructed and analyzed. For this purpose, cDNA libraries from ...

    Authors: Ekrem Dündar, Öznur Suakar, Turgay Unver and Ayhan Dagdelen
    Citation: BMC Genomics 2013 14:219
    Content type: Research article Published on:

  25. Vascular system formation has been studied through molecular and genetic approaches in Arabidopsis, a herbaceous dicot that is used as a model system. Different vascular systems have developed in other plants suc...

    Authors: Peng Xu, Yimeng Kong, Xuan Li and Laigeng Li
    Citation: BMC Genomics 2013 14:217
    Content type: Research article Published on:

  26. Transcription factors (TF) play a crucial role in regulating gene expression and are fit to regulate diverse cellular processes by interacting with other proteins. A TF named calmodulin binding transcription a...

    Authors: Neha Pandey, Alok Ranjan, Poonam Pant, Rajiv K Tripathi, Farha Ateek, Haushilla P Pandey, Uday V Patre and Samir V Sawant
    Citation: BMC Genomics 2013 14:216
    Content type: Research article Published on:

  27. Mammalian genes are regulated through the action of multiple regulatory elements, often distributed across large regions. The mechanisms that control the integration of these diverse inputs into specific gene ...

    Authors: Chao-Kung Chen, Orsolya Symmons, Veli Vural Uslu, Taro Tsujimura, Sandra Ruf, Damian Smedley and François Spitz
    Citation: BMC Genomics 2013 14:215
    Content type: Database Published on:

  29. Due to the constantly growing number of sequenced microbial genomes, comparative genomics has been playing a major role in the investigation of regulatory interactions in bacteria. Regulon inference mostly rem...

    Authors: Michael J Cipriano, Pavel N Novichkov, Alexey E Kazakov, Dmitry A Rodionov, Adam P Arkin, Mikhail S Gelfand and Inna Dubchak
    Citation: BMC Genomics 2013 14:213
    Content type: Database Published on:

  30. Although Candida albicans and Candida dubliniensis are most closely related, both species behave significantly different with respect to morphogenesis and virulence. In order to gain further insight into the dive...

    Authors: Christian Grumaz, Stefan Lorenz, Philip Stevens, Elena Lindemann, Ulrike Schöck, Julia Retey, Steffen Rupp and Kai Sohn
    Citation: BMC Genomics 2013 14:212
    Content type: Research article Published on:

  32. Phosphorus (P) is one of the essential but often limiting elements for plants. Based on transcriptional profiling we reported previously that more than 3,000 genes are differentially expressed between phosphat...

    Authors: Ping Lan, Wenfeng Li and Wolfgang Schmidt
    Citation: BMC Genomics 2013 14:210
    Content type: Research article Published on:

  34. Cotton, one of the world’s leading crops, is important to the world’s textile and energy industries, and is a model species for studies of plant polyploidization, cellulose biosynthesis and cell wall biogenesi...

    Authors: Mi-Kyung Lee, Yang Zhang, Meiping Zhang, Mark Goebel, Hee Jin Kim, Barbara A Triplett, David M Stelly and Hong-Bin Zhang
    Citation: BMC Genomics 2013 14:208
    Content type: Research article Published on:

  35. The microsporidian Encephalitozoon cuniculi possesses one of the most reduced and compacted eukaryotic genomes. Reduction in this intracellular parasite has affected major cellular machinery, including the loss o...

    Authors: Cameron J Grisdale, Lisa C Bowers, Elizabeth S Didier and Naomi M Fast
    Citation: BMC Genomics 2013 14:207
    Content type: Research article Published on:

  36. Adenosine-to-inosine (A-to-I) RNA editing is recognized as a cellular mechanism for generating both RNA and protein diversity. Inosine base pairs with cytidine during reverse transcription and therefore appear...

    Authors: Shanshan Zhu, Jian-Feng Xiang, Tian Chen, Ling-Ling Chen and Li Yang
    Citation: BMC Genomics 2013 14:206
    Content type: Research article Published on:

  37. Thousands of intragenic long interspersed element 1 sequences (LINE-1 elements or L1s) reside within genes. These intragenic L1 sequences are conserved and regulate the expression of their host genes. When L1 ...

    Authors: Wachiraporn Wanichnopparat, Kulachanya Suwanwongse, Piyapat Pin-on, Chatchawit Aporntewan and Apiwat Mutirangura
    Citation: BMC Genomics 2013 14:205
    Content type: Research article Published on:

  38. Evolutionary studies benefit from deep sequencing technologies that generate genomic and transcriptomic sequences from a variety of organisms. Genome sequencing and RNAseq have complementary strengths. In this...

    Authors: Yvan Wenger and Brigitte Galliot
    Citation: BMC Genomics 2013 14:204
    Content type: Research article Published on:

  39. Transcription factor binding is regulated by several interactions, primarily involving cis-element binding. These binding sites maintain specificity by means of their sequence, and other additional factors such a...

    Authors: Rajesh Mehrotra, Sachin Sethi, Ipshita Zutshi, Purva Bhalothia and Sandhya Mehrotra
    Citation: BMC Genomics 2013 14:203
    Content type: Research article Published on:

  40. Perennial ryegrass (Lolium perenne L.) is one of the most important forage and turf grass species of temperate regions worldwide. Its mitochondrial genome is inherited maternally and contains genes that can influ...

    Authors: Md Shofiqul Islam, Bruno Studer, Stephen L Byrne, Jacqueline D Farrell, Frank Panitz, Christian Bendixen, Ian Max Møller and Torben Asp
    Citation: BMC Genomics 2013 14:202
    Content type: Research article Published on:

  41. Eucalyptus is one of the most important sources of industrial cellulose. Three species of this botanical group are intensively used in breeding programs: E. globulus, E. grandis and E. urophylla. E. globulus is a...

    Authors: Marcela Mendes Salazar, Leandro Costa Nascimento, Eduardo Leal Oliveira Camargo, Danieli Cristina Gonçalves, Jorge Lepikson Neto, Wesley Leoricy Marques, Paulo José Pereira Lima Teixeira, Piotr Mieczkowski, Jorge Maurício Costa Mondego, Marcelo Falsarella Carazzolle, Ana Carolina Deckmann and Gonçalo Amarante Guimarães Pereira
    Citation: BMC Genomics 2013 14:201
    Content type: Research article Published on:

  42. Streptococcus infantarius subsp. infantarius (Sii) belongs to the Streptococcus bovis/Streptococcus equinus complex associated with several human and animal infections. Sii is a predominant bacterium in spontaneo...

    Authors: Christoph Jans, Rainer Follador, Mira Hochstrasser, Christophe Lacroix, Leo Meile and Marc J A Stevens
    Citation: BMC Genomics 2013 14:200
    Content type: Research article Published on:

  43. Alternative splicing (AS) is a major mechanism for modulating gene expression of an organism, allowing the synthesis of several structurally and functionally distinct mRNAs and protein isoforms from a unique g...

    Authors: Francisco Hernández-Torres, Alberto Rastrojo and Begoña Aguado
    Citation: BMC Genomics 2013 14:199
    Content type: Research article Published on:

  44. The European spruce bark beetle, Ips typographus, and the North American mountain pine beetle, Dendroctonus ponderosae (Coleoptera: Curculionidae: Scolytinae), are severe pests of coniferous forests. Both bark be...

    Authors: Martin N Andersson, Ewald Grosse-Wilde, Christopher I Keeling, Jonas M Bengtsson, Macaire MS Yuen, Maria Li, Ylva Hillbur, Jörg Bohlmann, Bill S Hansson and Fredrik Schlyter
    Citation: BMC Genomics 2013 14:198
    Content type: Research article Published on:

  45. Fusarium head blight (FHB), caused mainly by Fusarium graminearum (Fg) Schwabe (teleomorph: Gibberellazeae Schwble), brings serious damage to wheat production. Chinese wheat landrace Wangshuibai is one of the mos...

    Authors: Jin Xiao, Xiahong Jin, Xinping Jia, Haiyan Wang, Aizhong Cao, Weiping Zhao, Haiyan Pei, Zhaokun Xue, Liqiang He, Qiguang Chen and Xiue Wang
    Citation: BMC Genomics 2013 14:197
    Content type: Research article Published on:

  46. Association analysis using genome-wide expression quantitative trait locus (eQTL) data investigates the effect that genetic variation has on cellular pathways and leads to the discovery of candidate regulators...

    Authors: Ross E Curtis, Seyoung Kim, John L Woolford Jr, Wenjie Xu and Eric P Xing
    Citation: BMC Genomics 2013 14:196
    Content type: Research article Published on:

  47. The transition from the vegetative mycelium to the primordium during fruiting body development is the most complex and critical developmental event in the life cycle of many basidiomycete fungi. Understanding ...

    Authors: Chi Keung Cheng, Chun Hang Au, Sarah K Wilke, Jason E Stajich, Miriam E Zolan, Patricia J Pukkila and Hoi Shan Kwan
    Citation: BMC Genomics 2013 14:195
    Content type: Research article Published on:

  48. In Piedmontese cattle the double-muscled phenotype is an inherited condition associated to a point mutation in the myostatin (MSTN) gene. The Piedmontese MSTN missense mutation G938A is translated to C313Y myo...

    Authors: Silvia Miretti, Eugenio Martignani, Paolo Accornero and Mario Baratta
    Citation: BMC Genomics 2013 14:194
    Content type: Research article Published on:

  49. Human blood develops from self-renewing hematopoietic stem cells to terminal lineages and necessitates regulator and effector gene expression changes; each cell type specifically expresses a subset of genes to...

    Authors: Brian J Abraham, Kairong Cui, Qingsong Tang and Keji Zhao
    Citation: BMC Genomics 2013 14:193
    Content type: Research article Published on:

  50. Respiratory syncytial virus (RSV) is an important cause of lower respiratory tract infection in young children. The degree of disease severity is determined by the host response to infection. Lung macrophages ...

    Authors: Laxmi Iyer Ravi, Liang Li, Richard Sutejo, Hui Chen, Pui San Wong, Boon Huan Tan and Richard J Sugrue
    Citation: BMC Genomics 2013 14:190
    Content type: Research article Published on:

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BMC Genomics

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