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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  6. 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:

  7. 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:

  8. 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:

  10. 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:

  11. 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:

  13. 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:

  15. 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:

  16. 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:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  21. 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:

  22. 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:

  23. 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:

  24. 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:

  25. 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:

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  31. The genus Lens comprises a range of closely related species within the galegoid clade of the Papilionoideae family. The clade includes other important crops (e.g. chickpea and pea) as well as a sequenced model le...

    Authors: Andrew G Sharpe, Larissa Ramsay, Lacey-Anne Sanderson, Michael J Fedoruk, Wayne E Clarke, Rong Li, Sateesh Kagale, Perumal Vijayan, Albert Vandenberg and Kirstin E Bett
    Citation: BMC Genomics 2013 14:192
    Content type: Research article Published on:

  32. The genetic heterogeneity of sensorineural hearing loss is a major hurdle to the efficient discovery of disease-causing genes. We designed a multiphasic analysis of copy number variation (CNV), linkage, and si...

    Authors: Gibeom Park, Jungsoo Gim, Ah Reum Kim, Kyu-Hee Han, Hyo-Sang Kim, Seung-Ha Oh, Taesung Park, Woong-Yang Park and Byung Yoon Choi
    Citation: BMC Genomics 2013 14:191
    Content type: Research article Published on:

  33. 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:

  34. Protein translocation across membranes is a central process in all cells. In the past decades the molecular composition of the translocation systems in the membranes of the endoplasmic reticulum, peroxisomes, ...

    Authors: Puneet Paul, Stefan Simm, Andreas Blaumeiser, Klaus-Dieter Scharf, Sotirios Fragkostefanakis, Oliver Mirus and Enrico Schleiff
    Citation: BMC Genomics 2013 14:189
    Content type: Research article Published on:

  35. Signals of danger and damage in the cytosol of cells are sensed by NOD-like receptors (NLRs), which are components of multiprotein complexes called inflammasomes. Inflammasomes activate caspase-1, resulting in...

    Authors: Inka Sastalla, Devorah Crown, Seth L Masters, Andrew McKenzie, Stephen H Leppla and Mahtab Moayeri
    Citation: BMC Genomics 2013 14:188
    Content type: Research article Published on:

  36. MicroRNAs (miRNAs) are small non-coding RNAs that play critical roles in regulating post transcriptional gene expression. Gall midges encompass a large group of insects that are of economic importance and also...

    Authors: Chitvan Khajuria, Christie E Williams, Mustapha El Bouhssini, R Jeff Whitworth, Stephen Richards, Jeffrey J Stuart and Ming-Shun Chen
    Citation: BMC Genomics 2013 14:187
    Content type: Research article Published on:

  37. Microsporidian Nosema bombycis has received much attention because the pébrine disease of domesticated silkworms results in great economic losses in the silkworm industry. So far, no effective treatment could be ...

    Authors: Guoqing Pan, Jinshan Xu, Tian Li, Qingyou Xia, Shao-Lun Liu, Guojie Zhang, Songgang Li, Chunfeng Li, Handeng Liu, Liu Yang, Tie Liu, Xi Zhang, Zhengli Wu, Wei Fan, Xiaoqun Dang, Heng Xiang…
    Citation: BMC Genomics 2013 14:186
    Content type: Research article Published on:

  38. The African annual fish Nothobranchius furzeri has over recent years been established as a model species for ageing-related studies. This is mainly based on its exceptionally short lifespan and the presence of ty...

    Authors: Andreas Petzold, Kathrin Reichwald, Marco Groth, Stefan Taudien, Nils Hartmann, Steffen Priebe, Dmitry Shagin, Christoph Englert and Matthias Platzer
    Citation: BMC Genomics 2013 14:185
    Content type: Research article Published on:

  39. MicroRNAs (miRNAs), a group of short non-coding RNAs that negatively regulate gene expression, have recently emerged as potential modulators of cellular response to ionizing radiations both in vitro and in vivo i...

    Authors: Nicolas Joly-Tonetti, José Viñuelas, Olivier Gandrillon and Jérôme Lamartine
    Citation: BMC Genomics 2013 14:184
    Content type: Research article Published on:

  40. Toxoplasmosis is caused by the apicomplexan parasite Toxoplasma gondii and can be acquired either congenitally or via the oral route. In the latter case, transmission is mediated by two distinct invasive stages, ...

    Authors: Alessia Possenti, Federica Fratini, Luca Fantozzi, Edoardo Pozio, Jitender P Dubey, Marta Ponzi, Elisabetta Pizzi and Furio Spano
    Citation: BMC Genomics 2013 14:183
    Content type: Research article Published on:

  41. Endothelial progenitor cells (EPCs) play a fundamental role in post-natal vascular repair. Currently EPCs are defined as either early and late EPCs based on their biological properties and their time of appear...

    Authors: Cheng-Chung Cheng, Shing-Jyh Chang, Yu-Neng Chueh, Tse-Shun Huang, Po-Hsun Huang, Shu-Meng Cheng, Tsung-Neng Tsai, Jaw-Wen Chen and Hsei-Wei Wang
    Citation: BMC Genomics 2013 14:182
    Content type: Research article Published on:

  42. Simultaneous isolation of nucleic acids and proteins from a single biological sample facilitates meaningful data interpretation and reduces time, cost and sampling errors. This is particularly relevant for rar...

    Authors: André ES Simões, Diane M Pereira, Joana D Amaral, Ana F Nunes, Sofia E Gomes, Pedro M Rodrigues, Adrian C Lo, Rudi D'Hooge, Clifford J Steer, Stephen N Thibodeau, Pedro M Borralho and Cecília MP Rodrigues
    Citation: BMC Genomics 2013 14:181
    Content type: Methodology article Published on:

  43. Genomic resources for plant and animal species that are under exploitation primarily for human consumption are increasingly important, among other things, for understanding physiological processes and for esta...

    Authors: Laia Ribas, Belén G Pardo, Carlos Fernández, José Antonio Álvarez-Diós, Antonio Gómez-Tato, María Isabel Quiroga, Josep V Planas, Ariadna Sitjà-Bobadilla, Paulino Martínez and Francesc Piferrer
    Citation: BMC Genomics 2013 14:180
    Content type: Research article Published on:

  44. Based on their function in cancer micro(mi)RNAs are often grouped as either tumor suppressors or oncogenes. However, miRNAs regulate multiple tumor relevant signaling pathways raising the question whether two ...

    Authors: Youjia Hua, Niels Larsen, Shanker Kalyana-Sundaram, Jørgen Kjems, Arul M Chinnaiyan and Marcus E Peter
    Citation: BMC Genomics 2013 14:179
    Content type: Research article Published on:

  45. The gilthead sea bream (Sparus aurata) is the main fish species cultured in the Mediterranean area and constitutes an interesting model of research. Nevertheless, transcriptomic and genomic data are still scarce ...

    Authors: Josep A Calduch-Giner, Azucena Bermejo-Nogales, Laura Benedito-Palos, Itziar Estensoro, Gabriel Ballester-Lozano, Ariadna Sitjà-Bobadilla and Jaume Pérez-Sánchez
    Citation: BMC Genomics 2013 14:178
    Content type: Research article Published on:

  46. The species of T. harzianum are well known for their biocontrol activity against many plant pathogens. However, there is a lack of studies concerning its use as a biological control agent against F. solani, a pat...

    Authors: Pabline Marinho Vieira, Alexandre Siqueira Guedes Coelho, Andrei Stecca Steindorff, Saulo José Linhares de Siqueira, Roberto do Nascimento Silva and Cirano José Ulhoa
    Citation: BMC Genomics 2013 14:177
    Content type: Research article Published on:

  47. Microsatellites are widely used for many genetic studies. In contrast to single nucleotide polymorphism (SNP) and genotyping-by-sequencing methods, they are readily typed in samples of low DNA quality/concentr...

    Authors: Deborah A Dawson, Alexander D Ball, Lewis G Spurgin, David Martín-Gálvez, Ian R K Stewart, Gavin J Horsburgh, Jonathan Potter, Mercedes Molina-Morales, Anthony W J Bicknell, Stephanie A J Preston, Robert Ekblom, Jon Slate and Terry Burke
    Citation: BMC Genomics 2013 14:176
    Content type: Methodology article Published on:

  49. The functional and evolutionary diversification of insect cytochrome P450s (CYPs) shaped the success of insects. CYPs constitute one of the largest and oldest gene superfamilies that are found in virtually all...

    Authors: Fang Zhu, Timothy W Moural, Kapil Shah and Subba Reddy Palli
    Citation: BMC Genomics 2013 14:174
    Content type: Research article Published on:

  50. A unique feature of fish is that new muscle fibres continue to be produced throughout much of the life cycle; a process termed muscle hyperplasia. In trout, this process begins in the late embryo stage and occ...

    Authors: Pierre-Yves Rescan, Jerome Montfort, Alain Fautrel, Cécile Rallière and Veronique Lebret
    Citation: BMC Genomics 2013 14:173
    Content type: Research article Published on:

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BMC Genomics

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