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1399 result(s) within Volume 15 of BMC Genomics

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  1. Chromatin remodeling is crucial for proper programing of developmental gene expression. Recent work provides a dynamic view of post-translational histone modifications during differentiation; however there is ...

    Authors: Akshay Shah, Anja Oldenburg and Philippe Collas
    Citation: BMC Genomics 2014 15:1186
    Content type: Research article Published on:

  2. Cyanothece sp. PCC 7822 is an excellent cyanobacterial model organism with great potential to be applied as a biocatalyst for the production of high value compounds. Like other unicellular diazotrophic cyanobacte...

    Authors: David Welkie, Xiaohui Zhang, Meng Lye Markillie, Ronald Taylor, Galya Orr, Jon Jacobs, Ketaki Bhide, Jyothi Thimmapuram, Marina Gritsenko, Hugh Mitchell, Richard D Smith and Louis A Sherman
    Citation: BMC Genomics 2014 15:1185
    Content type: Research article Published on:

  3. The Bacillus genus of Firmicutes bacteria is ubiquitous in nature and includes one of the best characterized model organisms, B. subtilis, as well as medically significant human pathogens, the most notorious bein...

    Authors: Julianne H Grose, Garrett L Jensen, Sandra H Burnett and Donald P Breakwell
    Citation: BMC Genomics 2014 15:1184
    Content type: Erratum Published on:

    The original article was published in BMC Genomics 2014 15:855

  4. Gonad differentiation is an essential function for all sexually reproducing species, and many aspects of these developmental processes are highly conserved among the metazoa. The colonial ascidian, Botryllus schl...

    Authors: Delany Rodriguez, Erin N Sanders, Kelsea Farell, Adam D Langenbacher, Daryl A Taketa, Michelle Rae Hopper, Morgan Kennedy, Andrew Gracey and Anthony W De Tomaso
    Citation: BMC Genomics 2014 15:1183
    Content type: Research article Published on:

  5. Earlier studies were focused on the genetics of temperate and tropical maize under drought. We identified genetic loci and their association with functional mechanisms in 240 accessions of subtropical maize us...

    Authors: Nepolean Thirunavukkarasu, Firoz Hossain, Kanika Arora, Rinku Sharma, Kaliyugam Shiriga, Swati Mittal, Sweta Mohan, Pottekatt Mohanlal Namratha, Sreelatha Dogga, Tikka Shobha Rani, Sumalini Katragadda, Abhishek Rathore, Trushar Shah, Trilochan Mohapatra and Hari Shankar Gupta
    Citation: BMC Genomics 2014 15:1182
    Content type: Research article Published on:

  6. Transcriptogram profiling is a method to present and analyze transcription data in a genome-wide scale that reduces noise and facilitates biological interpretation. An ordered gene list is produced, such that ...

    Authors: Samoel RM da Silva, Gabriel C Perrone, João M Dinis and Rita MC de Almeida
    Citation: BMC Genomics 2014 15:1181
    Content type: Research article Published on:

  7. With the development of several new technologies using synthetic biology, it is possible to engineer genetically intractable organisms including Mycoplasma mycoides subspecies capri (Mmc), by cloning the intact b...

    Authors: Suchismita Chandran, Vladimir N Noskov, Thomas H Segall-Shapiro, Li Ma, Caitlin Whiteis, Carole Lartigue, Joerg Jores, Sanjay Vashee and Ray-Yuan Chuang
    Citation: BMC Genomics 2014 15:1180
    Content type: Methodology article Published on:

  8. Haemophilus parasuis is the etiologic agent of Glässer’s disease in pigs and causes devastating losses to the farming industry. Whilst some hyper-virulent isolates have been described, the relationship between ge...

    Authors: Kate J Howell, Lucy A Weinert, Roy R Chaudhuri, Shi-Lu Luan, Sarah E Peters, Jukka Corander, David Harris, Øystein Angen, Virginia Aragon, Albert Bensaid, Susanna M Williamson, Julian Parkhill, Paul R Langford, Andrew N Rycroft, Brendan W Wren, Matthew T G Holden…
    Citation: BMC Genomics 2014 15:1179
    Content type: Research article Published on:

  9. In the competing endogenous RNA (ceRNA) hypothesis, different transcripts communicate through a competition for their common targeting microRNAs (miRNAs). Individual examples have clearly shown the functional ...

    Authors: Danny Kit-Sang Yip, Iris K Pang and Kevin Y Yip
    Citation: BMC Genomics 2014 15:1178
    Content type: Methodology article Published on:

  10. Mutations in three functionally diverse genes cause Rett Syndrome. Although the functions of Forkhead box G1 (FOXG1), Methyl CpG binding protein 2 (MECP2) and Cyclin-dependent kinase-like 5 (CDKL5) have been stud...

    Authors: Morana Vitezic, Nicolas Bertin, Robin Andersson, Leonard Lipovich, Hideya Kawaji, Timo Lassmann, Albin Sandelin, Peter Heutink, Dan Goldowitz, Thomas Ha, Peter Zhang, Annarita Patrizi, Michela Fagiolini, Alistair RR Forrest, Piero Carninci and Alka Saxena
    Citation: BMC Genomics 2014 15:1177
    Content type: Research article Published on:

  11. Atherosclerosis is a progressive disease characterized by inflammation and accumulation of lipids in vascular tissue. Porphyromonas gingivalis (Pg) and Chlamydia pneumoniae (Cp) are associated with inflammatory a...

    Authors: Carolyn D Kramer, Ellen O Weinberg, Adam C Gower, Xianbao He, Samrawit Mekasha, Connie Slocum, Lea M Beaulieu, Lee Wetzler, Yuriy Alekseyev, Frank C Gibson III, Jane E Freedman, Robin R Ingalls and Caroline A Genco
    Citation: BMC Genomics 2014 15:1176
    Content type: Research article Published on:

  12. 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:

  13. 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:

  15. 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:

  18. Cell proliferation is a hallmark of cancer and depends on complex signaling networks that are chiefly supported by protein kinase activities. Therapeutic strategies have been used to target specific kinases bu...

    Authors: Philippe Nizard, Frédéric Ezan, Dominique Bonnier, Nolwenn Le Meur, Sophie Langouët, Georges Baffet, Yannick Arlot-Bonnemains and Nathalie Théret
    Citation: BMC Genomics 2014 15:1169
    Content type: Research article Published on:

  19. 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:

  20. Supplementation of broiler chicken diets with probiotics may improve carcass characteristics and meat quality. However, the underlying molecular mechanism remains unclear. In the present study, 2D-DIGE-based p...

    Authors: Aijuan Zheng, Jianjie Luo, Kun Meng, Jianke Li, Shu Zhang, Ke Li, Guohua Liu, Huiyi Cai, Wayne L Bryden and Bin Yao
    Citation: BMC Genomics 2014 15:1167
    Content type: Research article Published on:

  21. 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:

  22. Muscle ageing contributes to both loss of functional autonomy and increased morbidity. Muscle atrophy accelerates after 50 years of age, but the mechanisms involved are complex and likely result from the alter...

    Authors: Marine Gueugneau, Cécile Coudy-Gandilhon, Ophélie Gourbeyre, Christophe Chambon, Lydie Combaret, Cécile Polge, Daniel Taillandier, Didier Attaix, Bertrand Friguet, Andrea B Maier, Gillian Butler-Browne and Daniel Béchet
    Citation: BMC Genomics 2014 15:1165
    Content type: Research article Published on:

  23. 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:

  24. 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:

  25. 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:

  26. 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:

  27. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  33. 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:

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  39. 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:

  40. 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:

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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

  48. 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

  49. 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

  50. 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

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