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  1. The initiation of translation in eukaryotes is supported by the action of several eukaryotic Initiation Factors (eIFs). The largest of these is eIF3, comprising of up to thirteen polypeptides (eIF3a through eI...

    Authors: Antonio M Rezende, Ludmila A Assis, Eduardo C Nunes, Tamara D da Costa Lima, Fabricio K Marchini, Eden R Freire, Christian RS Reis and Osvaldo P de Melo Neto
    Citation: BMC Genomics 2014 15:1175
    Content type: Research article Published on:

  2. DNA methylation is an important epigenetic mechanism in several human diseases, most notably cancer. The quantitative analysis of DNA methylation patterns has the potential to serve as diagnostic and prognosti...

    Authors: Nicholas Redshaw, Jim F Huggett, Martin S Taylor, Carole A Foy and Alison S Devonshire
    Citation: BMC Genomics 2014 15:1174
    Content type: Research article Published on:

  3. Patient-derived tumor xenografts in mice are widely used in cancer research and have become important in developing personalized therapies. When these xenografts are subject to DNA sequencing, the samples coul...

    Authors: Kai-Yuen Tso, Sau Dan Lee, Kwok-Wai Lo and Kevin Y Yip
    Citation: BMC Genomics 2014 15:1172
    Content type: Methodology article Published on:

  5. Toxoplasma gondii is a widespread protozoan parasite of animals that causes zoonotic disease in humans. Three clonal variants predominate in North America and Europe, while South American strains are genetically ...

    Authors: Asis Khan, Jahangheer S Shaik, Michael Behnke, Qiuling Wang, Jitender P Dubey, Hernan A Lorenzi, James W Ajioka, Benjamin M Rosenthal and L David Sibley
    Citation: BMC Genomics 2014 15:1168
    Content type: Research article Published on:

  6. The protist Plasmodiophora brassicae is a biotrophic soil-borne pathogen that causes clubroot on Brassica crops worldwide. Clubroot disease is a serious threat to the 8 M ha of canola (Brassica napus) grown annua...

    Authors: Mingguang Chu, Tao Song, Kevin C Falk, Xingguo Zhang, Xunjia Liu, Adrian Chang, Rachid Lahlali, Linda McGregor, Bruce D Gossen, Fengqun Yu and Gary Peng
    Citation: BMC Genomics 2014 15:1166
    Content type: Research article Published on:

  7. Bovine respiratory disease complex (BRDC) is an infectious disease of cattle that is caused by a combination of viral and/or bacterial pathogens. Selection for cattle with reduced susceptibility to respiratory...

    Authors: Holly L Neibergs, Christopher M Seabury, Andrzej J Wojtowicz, Zeping Wang, Erik Scraggs, Jennifer N Kiser, Mahesh Neupane, James E Womack, Alison Van Eenennaam, Gerald Robert Hagevoort, Terry W Lehenbauer, Sharif Aly, Jessica Davis and Jeremy F Taylor
    Citation: BMC Genomics 2014 15:1164
    Content type: Research article Published on:

  8. Acinetobacter baumannii is an important nosocomial pathogen that poses a serious health threat to immune-compromised patients. Due to its rapid ability to develop multidrug resistance (MDR), A. baumannii has incr...

    Authors: Fei Liu, Yuying Zhu, Yong Yi, Na Lu, Baoli Zhu and Yongfei Hu
    Citation: BMC Genomics 2014 15:1163
    Content type: Research article Published on:

  9. Large-scale RNAi screening has become an important technology for identifying genes involved in biological processes of interest. However, the quality of large-scale RNAi screening is often deteriorated by off...

    Authors: Pauli Rämö, Anna Drewek, Cécile Arrieumerlou, Niko Beerenwinkel, Houchaima Ben-Tekaya, Bettina Cardel, Alain Casanova, Raquel Conde-Alvarez, Pascale Cossart, Gábor Csúcs, Simone Eicher, Mario Emmenlauer, Urs Greber, Wolf-Dietrich Hardt, Ari Helenius, Christoph Kasper…
    Citation: BMC Genomics 2014 15:1162
    Content type: Research article Published on:

  10. The recent emergence of a novel coronavirus in the Middle East (designated MERS-CoV) is a reminder of the zoonotic and pathogenic potential of emerging coronaviruses in humans. Clinical features of Middle East...

    Authors: Christian Selinger, Jennifer Tisoncik-Go, Vineet D Menachery, Sudhakar Agnihothram, G Lynn Law, Jean Chang, Sara M Kelly, Pavel Sova, Ralph S Baric and Michael G Katze
    Citation: BMC Genomics 2014 15:1161
    Content type: Research article Published on:

  11. As our world becomes warmer, agriculture is increasingly impacted by rising soil salinity and understanding plant adaptation to salt stress can help enable effective crop breeding. Salt tolerance is a complex ...

    Authors: Maren L Friesen, Eric JB von Wettberg, Mounawer Badri, Ken S Moriuchi, Fathi Barhoumi, Peter L Chang, Sonia Cuellar-Ortiz, Matilde A Cordeiro, Wendy T Vu, Soumaya Arraouadi, Naceur Djébali, Kais Zribi, Yazid Badri, Stephanie S Porter, Mohammed Elarbi Aouani, Douglas R Cook…
    Citation: BMC Genomics 2014 15:1160
    Content type: Research article Published on:

  13. Cucumber, Cucumis sativus L., is an economically important vegetable crop which is processed or consumed fresh worldwide. However, the narrow genetic base in cucumber makes it difficult for constructing high-dens...

    Authors: Qingzhen Wei, Yunzhu Wang, Xiaodong Qin, Yunxia Zhang, Zhentao Zhang, Jing Wang, Ji Li, Qunfeng Lou and Jinfeng Chen
    Citation: BMC Genomics 2014 15:1158
    Content type: Research article Published on:

  14. Small RNA-guided transcriptional silencing (nuclear RNAi) is fundamental to genome integrity and epigenetic inheritance. Despite recent progress in identifying the capability and genetic requirements for nucle...

    Authors: Julie Zhouli Ni, Esteban Chen and Sam Guoping Gu
    Citation: BMC Genomics 2014 15:1157
    Content type: Research article Published on:

  15. Zoraptera, generally regarded as a member of Polyneoptera, represents one of the most enigmatic insect orders. Although phylogenetic analyses based on a wide array of morphological and/or nuclear data have bee...

    Authors: Chuan Ma, Yeying Wang, Chao Wu, Le Kang and Chunxiang Liu
    Citation: BMC Genomics 2014 15:1156
    Content type: Research article Published on:

  16. The genetic diversity of loci and mutations underlying hereditary hearing loss is an active area of investigation. To identify loci associated with predominantly non-syndromic sensorineural hearing loss, we pe...

    Authors: Rajini R Haraksingh, Fereshteh Jahanbani, Juan Rodriguez-Paris, Joel Gelernter, Kari C Nadeau, John S Oghalai, Iris Schrijver and Michael P Snyder
    Citation: BMC Genomics 2014 15:1155
    Content type: Research article Published on:

  17. The human neuroblastoma cell line, SH-SY5Y, is a commonly used cell line in studies related to neurotoxicity, oxidative stress, and neurodegenerative diseases. Although this cell line is often used as a cellul...

    Authors: Abhimanyu Krishna, Maria Biryukov, Christophe Trefois, Paul MA Antony, Rene Hussong, Jake Lin, Merja Heinäniemi, Gustavo Glusman, Sandra Köglsberger, Olga Boyd, Bart HJ van den Berg, Dennis Linke, David Huang, Kai Wang, Leroy Hood, Andreas Tholey…
    Citation: BMC Genomics 2014 15:1154
    Content type: Research article Published on:

  18. The tephritid fruit flies include a number of economically important pests of horticulture, with a large accumulated body of research on their biology and control. Amongst the Tephritidae, the genus Bactrocera, c...

    Authors: Anthony Stuart Gilchrist, Deborah CA Shearman, Marianne Frommer, Kathryn A Raphael, Nandan P Deshpande, Marc R Wilkins, William B Sherwin and John A Sved
    Citation: BMC Genomics 2014 15:1153
    Content type: Research article Published on:

  19. A RIL population between Solanum lycopersicum cv. Moneymaker and S. pimpinellifolium G1.1554 was genotyped with a custom made SNP array. Additionally, a subset of the lines was genotyped by sequencing (GBS).

    Authors: Marcela Víquez-Zamora, Myluska Caro, Richard Finkers, Yury Tikunov, Arnaud Bovy, Richard GF Visser, Yuling Bai and Sjaak van Heusden
    Citation: BMC Genomics 2014 15:1152
    Content type: Research article Published on:

  20. Small secreted proteins (SSPs) are employed by plant pathogenic fungi as essential strategic tools for their successful colonization. SSPs are often species-specific and so far only a few widely phylogenetical...

    Authors: Qiang Cheng, Haoran Wang, Bin Xu, Sheng Zhu, Lanxi Hu and Minren Huang
    Citation: BMC Genomics 2014 15:1151
    Content type: Research article Published on:

  21. Animal models of cancer are useful to generate complementary datasets for comparison to human tumor data. Insertional mutagenesis screens, such as those utilizing the Sleeping Beauty (SB) transposon system, provi...

    Authors: Jesse D Riordan, Luke J Drury, Ryan P Smith, Benjamin T Brett, Laura M Rogers, Todd E Scheetz and Adam J Dupuy
    Citation: BMC Genomics 2014 15:1150
    Content type: Methodology article Published on:

  22. Enteromyxosis caused by the intestinal myxozoan parasite Enteromyxum scophthalmi is a serious threat for turbot (Scophthalmus maximus, L.) aquaculture, causing severe catarrhal enteritis leading to a cachectic sy...

    Authors: Diego Robledo, Paolo Ronza, Peter W Harrison, Ana Paula Losada, Roberto Bermúdez, Belén G Pardo, María José Redondo, Ariadna Sitjà-Bobadilla, María Isabel Quiroga and Paulino Martínez
    Citation: BMC Genomics 2014 15:1149
    Content type: Research article Published on:

  24. Tall fescue (Festuca arundinacea Schreb.) is major cool-season forage and turf grass species worldwide, but high-temperature is a major environmental stress that dramatically threaten forage production and turf m...

    Authors: Tao Hu, Xiaoyan Sun, Xunzhong Zhang, Eviatar Nevo and Jinmin Fu
    Citation: BMC Genomics 2014 15:1147
    Content type: Research article Published on:

  25. Bacteriophages that infect the opportunistic pathogen Pseudomonas aeruginosa have been classified into several groups. One of them, which includes temperate phage particles with icosahedral heads and long flexibl...

    Authors: Adrián Cazares, Guillermo Mendoza-Hernández and Gabriel Guarneros
    Citation: BMC Genomics 2014 15:1146
    Content type: Research article Published on:

  26. Staphylococcus aureus is a human pathogen responsible for substantial morbidity and mortality through its ability to cause a number of human infections including bacteremia, pneumonia and soft tissue infections. ...

    Authors: Marcus B Jones, Christopher P Montgomery, Susan Boyle-Vavra, Kenneth Shatzkes, Rosslyn Maybank, Bryan C Frank, Scott N Peterson and Robert S Daum
    Citation: BMC Genomics 2014 15:1145
    Content type: Research article Published on:

  27. Identification of differentially expressed genes from transcriptomic studies is one of the most common mechanisms to identify tumor biomarkers. This approach however is not well suited to identify interaction ...

    Authors: Paul O’Reilly, Csaba Ortutay, Grainne Gernon, Enda O’Connell, Cathal Seoighe, Susan Boyce, Luis Serrano and Eva Szegezdi
    Citation: BMC Genomics 2014 15:1144
    Content type: Research article Published on:

  28. The 3′ splice site (SS) at the end of pre-mRNA introns has a consensus sequence (Y)nNYAG for constitutive splicing of mammalian genes. Deviation from this consensus could change or interrupt the usage of the spli...

    Authors: Muhammad Sohail, Wenguang Cao, Niaz Mahmood, Mike Myschyshyn, Say Pham Hong and Jiuyong Xie
    Citation: BMC Genomics 2014 15:1143
    Content type: Research article Published on:

  29. Geothermal areas are of great interest for the study of microbial communities. The results of such investigations can be used in a variety of fields (ecology, microbiology, medicine) to answer fundamental ques...

    Authors: Alexey S Rozanov, Alla V Bryanskaya, Tatiana K Malup, Irina A Meshcheryakova, Elena V Lazareva, Oksana P Taran, Timofey V Ivanisenko, Vladimir A Ivanisenko, Sergey M Zhmodik, Nikolay A Kolchanov and Sergey E Peltek
    Citation: BMC Genomics 2014 15(Suppl 12):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  30. Long-range chromatin interactions play an important role in transcription regulation. Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET) is an emerging technology that has unique advantag...

    Authors: Guoliang Li, Liuyang Cai, Huidan Chang, Ping Hong, Qiangwei Zhou, Ekaterina V Kulakova, Nikolay A Kolchanov and Yijun Ruan
    Citation: BMC Genomics 2014 15(Suppl 12):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  31. Typically, gene expression biomarkers are being discovered in course of high-throughput experiments, for example, RNAseq or microarray profiling. Analytic pipelines that extract so-called signatures suffer fro...

    Authors: Boris Veytsman, Lei Wang, Tiange Cui, Sergey Bruskin and Ancha Baranova
    Citation: BMC Genomics 2014 15(Suppl 12):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  32. We perform the theoretical analysis of a gene network sub-system, composed of a feed-forward loop, in which the upstream transcription factor regulates the target gene via two parallel pathways: directly, and ...

    Authors: Maria A Duk, Maria G Samsonova and Alexander M Samsonov
    Citation: BMC Genomics 2014 15(Suppl 12):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  33. Affymetrix microarray technology allows one to investigate expression of thousands of genes simultaneously upon a variety of conditions. In a popular U133A microarray platform, the expression of 37% of genes i...

    Authors: Andrey Marakhonov, Nataliya Sadovskaya, Ivan Antonov, Ancha Baranova and Mikhail Skoblov
    Citation: BMC Genomics 2014 15(Suppl 12):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  34. Biological processes are usually distributed over various intracellular compartments. Proteins from diverse cellular compartments are often involved in similar signaling networks. However, the difference in th...

    Authors: Olga Vasil'evna Popik, Olga Vladimirovna Saik, Evgeny Dmitrievich Petrovskiy, Björn Sommer, Ralf Hofestädt, Inna Nikolaevna Lavrik and Vladimir Aleksandrovich Ivanisenko
    Citation: BMC Genomics 2014 15(Suppl 12):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  35. The detailed analysis of transcriptional regulation is crucially important for understanding biological processes. The gap gene network in Drosophila attracts large interest among researches studying mechanisms o...

    Authors: Konstantin Kozlov, Vitaly Gursky, Ivan Kulakovskiy and Maria Samsonova
    Citation: BMC Genomics 2014 15(Suppl 12):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  36. Ionizing radiation in low doses is the ubiquitous environmental factor with harmful stochastic effects. Formaldehyde is one of the most reactive household and industrial pollutants. Dioxins are persistent orga...

    Authors: Alexey Moskalev, Mikhail Shaposhnikov, Ekaterina Plyusnina, Sergey Plyusnin, Olga Shostal, Alexander Aliper and Alex Zhavoronkov
    Citation: BMC Genomics 2014 15(Suppl 12):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  37. Auxin responsive elements (AuxRE) were found in upstream regions of target genes for ARFs (Auxin response factors). While Chip-seq data for most of ARFs are still unavailable, prediction of potential AuxRE is ...

    Authors: Victoria V Mironova, Nadezda A Omelyanchuk, Daniil S Wiebe and Victor G Levitsky
    Citation: BMC Genomics 2014 15(Suppl 12):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  38. Etiology of complex disorders, such as cataract and neurodegenerative diseases including age-related macular degeneration (AMD), remains poorly understood due to the paucity of animal models, fully replicating...

    Authors: Elena E Korbolina, Nikita I Ershov, Leonid O Bryzgalov and Natalia G Kolosova
    Citation: BMC Genomics 2014 15(Suppl 12):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  39. Long-term space travel simulation experiments enabled to discover different aspects of human metabolism such as the complexity of NaCl salt balance. Detailed proteomics data were collected during the Mars105 i...

    Authors: Hans Binder, Henry Wirth, Arsen Arakelyan, Kathrin Lembcke, Evgeny S Tiys, Vladimir A Ivanisenko, Nikolay A Kolchanov, Alexey Kononikhin, Igor Popov, Evgeny N Nikolaev, Lyudmila Kh Pastushkova and Irina M Larina
    Citation: BMC Genomics 2014 15(Suppl 12):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  40. The life cycle of human immunodeficiency virus type-1 (HIV-1) makes possible the realization of regulatory strategies that can lead to complex dynamical behavior of the system. We analyze the strategy which is...

    Authors: Vitaly A Likhoshvai, Tamara M Khlebodarova, Sergei I Bazhan, Irina A Gainova, Valery A Chereshnev and Gennady A Bocharov
    Citation: BMC Genomics 2014 15(Suppl 12):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  41. The clustering of genes in a pathway and the co-location of functionally related genes is widely recognized in prokaryotes. We used these characteristics to predict the metabolic involvement for a Transcriptio...

    Authors: Ricardo Martí-Arbona, Fangping Mu, Kristy L Nowak-Lovato, Melinda S Wren, Clifford J Unkefer and Pat J Unkefer
    Citation: BMC Genomics 2014 15:1142
    Content type: Research article Published on:

  42. Chemoreception is based on the senses of smell and taste that are crucial for animals to find new food sources, shelter, and mates. The initial step in olfaction involves the translocation of odorants from the...

    Authors: Stefan Dippel, Georg Oberhofer, Jörg Kahnt, Lizzy Gerischer, Lennart Opitz, Joachim Schachtner, Mario Stanke, Stefan Schütz, Ernst A Wimmer and Sergio Angeli
    Citation: BMC Genomics 2014 15:1141
    Content type: Research article Published on:

  43. Top-down mass spectrometry plays an important role in intact protein identification and characterization. Top-down mass spectra are more complex than bottom-up mass spectra because they often contain many isot...

    Authors: Qiang Kou, Si Wu and Xiaowen Liu
    Citation: BMC Genomics 2014 15:1140
    Content type: Research article Published on:

  44. Acetogenic bacteria are able to use CO2 as terminal electron acceptor of an anaerobic respiration, thereby producing acetate with electrons coming from H2. Due to this feature, acetogens came into focus as platfo...

    Authors: Verena Hess, Anja Poehlein, Marie Charlotte Weghoff, Rolf Daniel and Volker Müller
    Citation: BMC Genomics 2014 15:1139
    Content type: Research article Published on:

  45. Highly parallel, ‘second generation’ sequencing technologies have rapidly expanded the number of bacterial whole genome sequences available for study, permitting the emergence of the discipline of population g...

    Authors: Holly B Bratcher, Craig Corton, Keith A Jolley, Julian Parkhill and Martin CJ Maiden
    Citation: BMC Genomics 2014 15:1138
    Content type: Methodology article Published on:

  46. Ashbya gossypii is a filamentous Saccharomycete used for the industrial production of riboflavin that has been recently explored as a host system for recombinant protein production. To gain insight into the prote...

    Authors: Tatiana Q Aguiar, Orquídea Ribeiro, Mikko Arvas, Marilyn G Wiebe, Merja Penttilä and Lucília Domingues
    Citation: BMC Genomics 2014 15:1137
    Content type: Research article Published on:

  47. The adult skeletal muscle is a plastic tissue with a remarkable ability to adapt to different levels of activity by altering its excitability, its contractile and metabolic phenotype and its mass. We previousl...

    Authors: Arjan P Palstra, Mireia Rovira, David Rizo-Roca, Joan Ramon Torrella, Herman P Spaink and Josep V Planas
    Citation: BMC Genomics 2014 15:1136
    Content type: Research article Published on:

  48. Vibrio parahaemolyticus is a Gram-negative halophilic bacterium. Infections with the bacterium could become systemic and can be life-threatening to immunocompromised individuals. Genome sequences of a few clinica...

    Authors: Lei Li, Hin-chung Wong, Wenyan Nong, Man Kit Cheung, Patrick Tik Wan Law, Kai Man Kam and Hoi Shan Kwan
    Citation: BMC Genomics 2014 15:1135
    Content type: Research article Published on:

  49. Teleost intestine is crucial for seawater acclimation by sensing osmolality of imbibed seawater and regulating drinking and water/ion absorption. Regulatory genes for transforming intestinal function have not ...

    Authors: Marty Kwok-Shing Wong, Haruka Ozaki, Yutaka Suzuki, Wataru Iwasaki and Yoshio Takei
    Citation: BMC Genomics 2014 15:1134
    Content type: Research article Published on:

  50. Sheepgrass (Leymus chinensis) is an important perennial forage grass across the Eurasian Steppe and is adaptable to various environmental conditions, but little is known about its molecular mechanism responding t...

    Authors: Xin Huang, Xianjun Peng, Lexin Zhang, Shuangyan Chen, Liqin Cheng and Gongshe Liu
    Citation: BMC Genomics 2014 15:1126
    Content type: Research article Published on:

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