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  1. Loss of virulence is a phenotypic adaptation commonly seen in prokaryotic and eukaryotic pathogens. This mechanism is not well studied, especially in organisms with multiple host and life cycle stages such as Bab...

    Authors: Monica J Pedroni, Kerry S Sondgeroth, Gina M Gallego-Lopez, Ignacio Echaide and Audrey OT Lau
    Citation: BMC Genomics 2013 14:763
    Content type: Research article Published on:

  2. Xanthomonads are plant-associated bacteria responsible for diseases on economically important crops. Xanthomonas fuscans subsp. fuscans (Xff) is one of the causal agents of common bacterial blight of bean. In thi...

    Authors: Armelle Darrasse, Sébastien Carrère, Valérie Barbe, Tristan Boureau, Mario L Arrieta-Ortiz, Sophie Bonneau, Martial Briand, Chrystelle Brin, Stéphane Cociancich, Karine Durand, Stéphanie Fouteau, Lionel Gagnevin, Fabien Guérin, Endrick Guy, Arnaud Indiana, Ralf Koebnik…
    Citation: BMC Genomics 2013 14:761
    Content type: Research article Published on:

  3. Plant calcium (Ca2+) signals are involved in a wide array of intracellular signalling pathways following pathogen invasion. Ca2+-binding sensory proteins such as Ca2+-dependent protein kinases (CPKs) have been pr...

    Authors: Chidananda Nagamangala Kanchiswamy, Tapan Kumar Mohanta, Andrea Capuzzo, Andrea Occhipinti, Francesca Verrillo, Massimo E Maffei and Mickael Malnoy
    Citation: BMC Genomics 2013 14:760
    Content type: Research article Published on:

  4. When the filamentous cyanobacterium Anabaena variabilis grows aerobically without combined nitrogen, some vegetative cells differentiate into N2-fixing heterocysts, while the other vegetative cells perform photos...

    Authors: Jeong-Jin Park, Sigal Lechno-Yossef, Coleman Peter Wolk and Claire Vieille
    Citation: BMC Genomics 2013 14:759
    Content type: Research article Published on:

  5. Fasting induces specific molecular and metabolic adaptions in most organisms. In biomedical research fasting is used in metabolic studies to synchronize nutritional states of study subjects. Because there is a...

    Authors: Michael Schupp, Fang Chen, Erika R Briggs, Shilpa Rao, Helmut J Pelzmann, Ariane R Pessentheiner, Juliane G Bogner-Strauss, Mitchell A Lazar, Don Baldwin and Andreas Prokesch
    Citation: BMC Genomics 2013 14:758
    Content type: Research article Published on:

  6. Our recent study showed the global physiological function of the differentially expressed genes of prostate cancer in Chinese patients was different from that of other non-Chinese populations. microRNA are est...

    Authors: Hui-chan He, Zhao-dong Han, Qi-shan Dai, Xiao-hui Ling, Xin Fu, Zhuo-yuan Lin, Ye-han Deng, Guo-qiang Qin, Chao Cai, Jia-hong Chen, Fu-neng Jiang, Xingyin Liu and Wei-de Zhong
    Citation: BMC Genomics 2013 14:757
    Content type: Research article Published on:

  7. Comparative genomics approaches help to shed light on evolutionary processes that shape differentiation between lineages. The nine-spined stickleback (Pungitius pungitius) is a closely related species of the ecol...

    Authors: Baocheng Guo, Frédéric JJ Chain, Erich Bornberg-Bauer, Erica H Leder and Juha Merilä
    Citation: BMC Genomics 2013 14:756
    Content type: Research article Published on:

  8. The genomes of multicellular eukaryotes are compartmentalized in mosaics of isochores, large and fairly homogeneous stretches of DNA that belong to a small number of families characterized by different average...

    Authors: Maria Costantini, Fernando Alvarez-Valin, Susan Costantini, Rosalia Cammarano and Giorgio Bernardi
    Citation: BMC Genomics 2013 14:755
    Content type: Research article Published on:

  9. Blunt snout bream (Megalobrama amblycephala) is an economically important fish species in the Chinese freshwater polyculture system for its delicacy and high economic value. MicroRNAs (miRNAs) play important role...

    Authors: Shaokui Yi, Ze-Xia Gao, Honghao Zhao, Cong Zeng, Wei Luo, Boxiang Chen and Wei-Min Wang
    Citation: BMC Genomics 2013 14:754
    Content type: Research article Published on:

  10. A hexaploidization event over 125 Mya underlies the evolutionary lineage of the majority of flowering plants, including very many species of agricultural importance. Half of these belong to the rosid subgroupi...

    Authors: Chunfang Zheng, Eric Chen, Victor A Albert, Eric Lyons and David Sankoff
    Citation: BMC Genomics 2013 14(Suppl 7):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 7

  11. The identification of proteins based on analysis of tandem mass spectrometry (MS/MS) data is a valuable tool that is not fully realized because of the difficulty in carrying out automated analysis of large num...

    Authors: Jason Gallia, Katelyn Lavrich, Anna Tan-Wilson and Patrick H Madden
    Citation: BMC Genomics 2013 14(Suppl 7):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 7

  12. Flow cytometry has been widely used for the diagnosis of various hematopoietic diseases. Although there have been advances in the number of biomarkers that can be analyzed simultaneously and technologies that ...

    Authors: Ming-Chih Shih, Shou-Hsuan Stephen Huang, Rachel Donohue, Chung-Che Chang and Youli Zu
    Citation: BMC Genomics 2013 14(Suppl 7):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 7

  14. AtPAP2 is a purple acid phosphatase that is targeted to both chloroplasts and mitochondria. Over-expression (OE) lines of AtPAP2 grew faster, produced more seeds, and contained higher leaf sucrose and glucose ...

    Authors: Feng Sun, Chao Liang, James Whelan, Jun Yang, Peng Zhang and Boon Leong Lim
    Citation: BMC Genomics 2013 14:752
    Content type: Research article Published on:

  15. Diapause is programmed developmental arrest coupled with the depression of metabolic activity and the enhancement of stress resistance. Pupal diapause is induced by environmental signals and is prepared during...

    Authors: Qi Zhang, Yu-Xuan Lu and Wei-Hua Xu
    Citation: BMC Genomics 2013 14:751
    Content type: Research article Published on:

  16. Peach [Prunus persica (L.) Batsch] is an economically important fruit crop that has become a genetic-genomic model for all Prunus species in the family Rosaceae. A doubled haploid reference genome sequence length...

    Authors: Jonathan Fresnedo-Ramírez, Pedro J Martínez-García, Dan E Parfitt, Carlos H Crisosto and Thomas M Gradziel
    Citation: BMC Genomics 2013 14:750
    Content type: Research article Published on:

  17. Two sibling members of the Anopheles gambiae species complex display notable differences in female blood meal preferences. An. gambiae s.s. has a well-documented preference for feeding upon human hosts, whereas A...

    Authors: David C Rinker, Xiaofan Zhou, Ronald Jason Pitts, Antonis Rokas and Laurence J Zwiebel
    Citation: BMC Genomics 2013 14:749
    Content type: Research article Published on:

  18. The Himalayan or Indian Mayapple (Podophyllum hexandrum Royle) produces podophyllotoxin, which is used in the production of semisynthetic anticancer drugs. High throughput transcriptome sequences or genomic seque...

    Authors: Dipto Bhattacharyya, Ragini Sinha, Saptarshi Hazra, Riddhi Datta and Sharmila Chattopadhyay
    Citation: BMC Genomics 2013 14:748
    Content type: Research article Published on:

  19. The relationship between fish health and muscle growth is critical for continued expansion of the aquaculture industry. The effect of immune stimulation on the expression of genes related to the energy balance...

    Authors: Nicholas J Pooley, Luca Tacchi, Christopher J Secombes and Samuel AM Martin
    Citation: BMC Genomics 2013 14:747
    Content type: Research article Published on:

  21. Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in prokaryotes is one of the critical tasks of modern genomics. Bacteria from different taxonomic groups, wh...

    Authors: Pavel S Novichkov, Alexey E Kazakov, Dmitry A Ravcheev, Semen A Leyn, Galina Y Kovaleva, Roman A Sutormin, Marat D Kazanov, William Riehl, Adam P Arkin, Inna Dubchak and Dmitry A Rodionov
    Citation: BMC Genomics 2013 14:745
    Content type: Database Published on:

  22. In the model eukaryote, Saccharomyces cerevisiae, previous experiments have identified those genes that exert the most significant control over cell growth rate. These genes are termed HFC for high flux control. ...

    Authors: Annette A Alcasabas, Michaela de Clare, Pınar Pir and Stephen G Oliver
    Citation: BMC Genomics 2013 14:744
    Content type: Research article Published on:

  23. Infectious bronchitis virus (IBV), a prototype of the Coronaviridae family, is an economically important causative agent of infectious bronchitis in chickens and causes an acute and highly contagious upper respir...

    Authors: Feng Cong, Xiaoli Liu, Zongxi Han, Yuhao Shao, Xiangang Kong and Shengwang Liu
    Citation: BMC Genomics 2013 14:743
    Content type: Research article Published on:

  24. Pectin methylesterases (PMEs) catalyze the demethylesterification of homogalacturonans in the cell wall; their activity is regulated in part by pectin methylesterase inhibitors (PMEIs). PME activity may result...

    Authors: David Pinzón-Latorre and Michael K Deyholos
    Citation: BMC Genomics 2013 14:742
    Content type: Research article Published on:

  25. The Grooved Carpet shell clam Ruditapes decussatus is the autochthonous European clam and the most appreciated from a gastronomic and economic point of view. The production is in decline due to several factors su...

    Authors: Ricardo B Leite, Massimo Milan, Alessandro Coppe, Stefania Bortoluzzi, António dos Anjos, Richard Reinhardt, Carlos Saavedra, Tomaso Patarnello, M Leonor Cancela and Luca Bargelloni
    Citation: BMC Genomics 2013 14:741
    Content type: Research article Published on:

  26. Williams syndrome transcription factor (WSTF) is a multifaceted protein that is involved in several nuclear processes, including replication, transcription, and the DNA damage response. WSTF participates in a ...

    Authors: Ashley E Culver-Cochran and Brian P Chadwick
    Citation: BMC Genomics 2013 14:740
    Content type: Research article Published on:

  27. Dengue is the most prevalent arboviral disease world-wide and its primary vector is the mosquito Aedes aegypti. The current lack of commercially-available vaccines makes control of vector populations the only eff...

    Authors: Mariangela Bonizzoni, Monica Britton, Osvaldo Marinotti, William Augustine Dunn, Joseph Fass and Anthony A James
    Citation: BMC Genomics 2013 14:739
    Content type: Research article Published on:

  28. The potential impact of genetically modified (GM) plants on human health has attracted much attention worldwide, and the issue remains controversial. This is in sharp contrast to the broad acceptance of plants...

    Authors: Lifen Gao, Yinghao Cao, Zhihui Xia, Guanghuai Jiang, Guozhen Liu, Weixiong Zhang and Wenxue Zhai
    Citation: BMC Genomics 2013 14:738
    Content type: Research article Published on:

  29. The interaction between insect pests and their host plants is a never-ending race of evolutionary adaption. Plants have developed an armament against insect herbivore attacks, and attackers continuously learn ...

    Authors: Birgit Kersten, Andrea Ghirardo, Jörg-Peter Schnitzler, Basem Kanawati, Philippe Schmitt-Kopplin, Matthias Fladung and Hilke Schroeder
    Citation: BMC Genomics 2013 14:737
    Content type: Research article Published on:

  30. Hepatocellular carcinoma (HCC) in young subjects is rare but more devastating. We hypothesize that genes and etiological pathways are unique to young HCC (yHCC; ≤40 years old at diagnosis) patients. We therefo...

    Authors: Hsei-Wei Wang, Tsung-Han Hsieh, SSu-Yi Huang, Gar-Yang Chau, Chien-Yi Tung, Chien-Wei Su and Jaw-Ching Wu
    Citation: BMC Genomics 2013 14:736
    Content type: Research article Published on:

  31. The implication of post-transcriptional regulation by microRNAs in molecular mechanisms underlying cancer disease is well documented. However, their interference at the cellular level is not fully explored. Fu...

    Authors: Patricia Severino, Liliane Santana Oliveira, Natalia Torres, Flavia Maziero Andreghetto, Maria de Fatima Guarizo Klingbeil, Raquel Moyses, Victor Wünsch-Filho, Fabio Daumas Nunes, Monica Beatriz Mathor, Alexandre Rossi Paschoal and Alan Mitchell Durham
    Citation: BMC Genomics 2013 14:735
    Content type: Research article Published on:

  32. Genetic linkage maps are important tools for many genetic applications including mapping of quantitative trait loci (QTLs), identifying DNA markers for fingerprinting, and map-based gene cloning. Carnation (Diant...

    Authors: Masafumi Yagi, Toshiya Yamamoto, Sachiko Isobe, Hideki Hirakawa, Satoshi Tabata, Koji Tanase, Hiroyasu Yamaguchi and Takashi Onozaki
    Citation: BMC Genomics 2013 14:734
    Content type: Research article Published on:

  33. Hypodontia, the congenital absence of one or a few teeth is one of the most common alterations of the human dentition. Familial hypodontia is caused by mutations in PAX9, Msx1 and Axin2 genes. Limited numbers of ...

    Authors: Eren Isman, Suleyman Nergiz, Hasan Acar and Zafer Sari
    Citation: BMC Genomics 2013 14:733
    Content type: Research article Published on:

  34. Codon usage analysis has been a classical topic for decades and has significances for studies of evolution, mRNA translation, and new gene discovery, etc. While the codon usage varies among different members o...

    Authors: Chao Feng, Chang-jie Xu, Yue Wang, Wen-li Liu, Xue-ren Yin, Xian Li, Ming Chen and Kun-song Chen
    Citation: BMC Genomics 2013 14:732
    Content type: Research article Published on:

  35. 4-Hydroxy-tamoxifen (4OHT) triggers Cre-mediated K-Ras removal in [H-Ras-/-;N-Ras-/-;K-Raslox/lox;RERTert/ert] fibroblasts, generating growth-arrested “Rasless” MEFs which are able to recover their proliferative ...

    Authors: Sami S Azrak, Alicia Ginel-Picardo, Matthias Drosten, Mariano Barbacid and Eugenio Santos
    Citation: BMC Genomics 2013 14:731
    Content type: Research article Published on:

  36. As consumers continue to request food products that have health advantages, it will be important for the livestock industry to supply a product that meet these demands. One such nutrient is fatty acids, which ...

    Authors: Mahdi Saatchi, Dorian J Garrick, Richard G Tait Jr, Mary S Mayes, Mary Drewnoski, Jon Schoonmaker, Clara Diaz, Don C Beitz and James M Reecy
    Citation: BMC Genomics 2013 14:730
    Content type: Research article Published on:

  37. It is generally agreed that horizontal gene transfer (HGT) is common in phagotrophic protists. However, the overall scale of HGT and the cumulative impact of acquired genes on the evolution of these organisms ...

    Authors: Jipei Yue, Guiling Sun, Xiangyang Hu and Jinling Huang
    Citation: BMC Genomics 2013 14:729
    Content type: Research article Published on:

  38. Data preprocessing is a major step in data mining. In data preprocessing, several known techniques can be applied, or new ones developed, to improve data quality such that the mining results become more accura...

    Authors: Ana T Winck, Karina S Machado, Osmar Norberto de Souza and Duncan D Ruiz
    Citation: BMC Genomics 2013 14(Suppl 6):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 6

  39. Lung cancer accounts for the highest number of cancer-related deaths worldwide. Early diagnosis significantly increases the disease-free survival rate and a large amount of effort has been expended in screenin...

    Authors: Debmalya Barh, Neha Jain, Sandeep Tiwari, John K Field, Elena Padin-Iruegas, Alvaro Ruibal, Rafael López, Michel Herranz, Antaripa Bhattacharya, Lucky Juneja, Cedric Viero, Artur Silva, Anderson Miyoshi, Anil Kumar, Kenneth Blum, Vasco Azevedo…
    Citation: BMC Genomics 2013 14(Suppl 6):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 6

  40. Current immunological bioinformatic approaches focus on the prediction of allele-specific epitopes capable of triggering immunogenic activity. The prediction of major histocompatibility complex (MHC) class I e...

    Authors: Anderson R Santos, Vanessa Bastos Pereira, Eudes Barbosa, Jan Baumbach, Josch Pauling, Richard Röttger, Meritxell Zurita Turk, Artur Silva, Anderson Miyoshi and Vasco Azevedo
    Citation: BMC Genomics 2013 14(Suppl 6):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 6

  41. The thymic epithelium is the major microenvironmental component of the thymus, the primary lymphoid organ responsible for the generation of T lymphocytes. Thymic epithelial cells (TEC) control intrathymic T ce...

    Authors: Daiane Cristina Ferreira Golbert, Eliane Correa-de-Santana, Marcelo Ribeiro-Alves, Ana Tereza Ribeiro de Vasconcelos and Wilson Savino
    Citation: BMC Genomics 2013 14(Suppl 6):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 6

  42. The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associate...

    Authors: Flávia A Miyazaki, Gabriela DA Guardia, Ricardo ZN Vêncio and Cléver RG de Farias
    Citation: BMC Genomics 2013 14(Suppl 6):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 6

  43. Nuclear receptors (NRs) are transcription factors which bind small hormones, whose evolutionary history and the presence of different functional surfaces makes them an interesting target for a correlation base...

    Authors: Marcelo Querino Lima Afonso, Leonardo Henrique França de Lima and Lucas Bleicher
    Citation: BMC Genomics 2013 14(Suppl 6):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 6

  44. Fusarium head blight (FHB) caused by Fusarium graminearum Schwabe is one of the most prevalent diseases of wheat (Triticum aestivum L.) and other small grain cereals. Resistance against the fungus is quantitative...

    Authors: Karl G Kugler, Gerald Siegwart, Thomas Nussbaumer, Christian Ametz, Manuel Spannagl, Barbara Steiner, Marc Lemmens, Klaus FX Mayer, Hermann Buerstmayr and Wolfgang Schweiger
    Citation: BMC Genomics 2013 14:728
    Content type: Research article Published on:

  45. 'Kuerlexiangli’ (Pyrus sinkiangensis Yu), a native pear of Xinjiang, China, is an important agricultural fruit and primary export to the international market. However, fruit with persistent calyxes affect fruit s...

    Authors: Xiaoxiao Qi, Jun Wu, Lifen Wang, Leiting Li, Yufen Cao, Luming Tian, Xingguang Dong and Shaoling Zhang
    Citation: BMC Genomics 2013 14:727
    Content type: Research article Published on:

  46. DNA repair is essential for the maintenance of genome stability in all living beings. Genome size as well as the repertoire and abundance of DNA repair components may vary among prokaryotic species. The bacter...

    Authors: Alexey Y Gorbachev, Gleb Y Fisunov, Mark Izraelson, Darya V Evsyutina, Pavel V Mazin, Dmitry G Alexeev, Olga V Pobeguts, Tatyana N Gorshkova, Sergey I Kovalchuk, Dmitry E Kamashev and Vadim M Govorun
    Citation: BMC Genomics 2013 14:726
    Content type: Research article Published on:

  47. Although the study of gene regulation via the action of specific microRNAs (miRNAs) has experienced a boom in recent years, the analysis of genome-wide interaction networks among miRNAs and respective targeted...

    Authors: Yury O Nunez, Jay M Truitt, Giorgio Gorini, Olga N Ponomareva, Yuri A Blednov, R Adron Harris and R Dayne Mayfield
    Citation: BMC Genomics 2013 14:725
    Content type: Research article Published on:

  48. The genetic basis of susceptibility to renal tumorigenesis has not yet been established in mouse strains. Mouse lines derived by bidirectional phenotypic selection on the basis of their maximal (AIRmax) or min...

    Authors: José Ricardo Jensen, Antonella Galvan, Andrea Borrego, Wafa Hanna Koury Cabrera, Orlando Garcia Ribeiro, Nancy Starobinas, Marcelo De Franco, Maurizio Colecchia, Alessia Bertolotti, Tommaso Antonio Dragani and Olga Célia Martinez Ibañez
    Citation: BMC Genomics 2013 14:724
    Content type: Research article Published on:

  49. Leishmania are obligated intracellular pathogens that replicate almost exclusively in macrophages. The outcome of infection depends largely on parasite pathogenicity and virulence but also on the activation statu...

    Authors: Imen Rabhi, Sameh Rabhi, Rym Ben-Othman, Mohamed Radhouane Aniba, Bernadette Trentin, David Piquemal, Béatrice Regnault and Lamia Guizani-Tabbane
    Citation: BMC Genomics 2013 14:723
    Content type: Research article Published on:

  50. Low temperature leads to major crop losses every year. Although several studies have been conducted focusing on diversity of cold tolerance level in multiple phenotypically divergent Arabidopsis thaliana (A. thal...

    Authors: Pankaj Barah, Naresh Doni Jayavelu, Simon Rasmussen, Henrik Bjørn Nielsen, John Mundy and Atle M Bones
    Citation: BMC Genomics 2013 14:722
    Content type: Research article Published on:

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BMC Genomics

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