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Bioinformatics on environment microbial resources

Bioinformatics is the management, ie. storing, retrieving, organizing and analyzing, of biological information, using advanced computer technology be developing suitable software tools.

 

 

1)Title: Advances in the application of high-throughput sequencing in invertebrate virology
Author: R. van Aerle, E.M. Santos
Journal: Journal of Invertebrate Pathology
Year: 2017
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2)Title: Conversion of grassland to arable decreases microbial diversity and alters community composition
Author: Katherine E. French, Andrzej Tkacz, Lindsay A. Turnbull
Journal: Applied Soil Ecology
Year: 2017
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3)Title: Depth-resolved microbial community analyses in two contrasting soil cores contaminated by antimony and arsenic
Author: Enzong Xiao, Valdis Krumins, Tangfu Xiao, Yiran Dong, Song Tang, Zengping Ning, Zhengyu Huang, Weimin Sun
Journal: Environmental Pollution
Year: 2017
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4)Title: Impacts of conversion from secondary forests to larch plantations on the structure and function of microbial communities
Author: Weiwei Zhang, Zhitang Lu, Kai Yang, Jiaojun Zhu
Journal: Applied Soil Ecology
Year: 2017
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5)Title: Mechanisms of microbial community structure and biofouling shifts under multivalent cations stress in membrane bioreactors
Author: Yu Miao, Xuechao Guo, Wei Jiang, Xu-Xiang Zhang, Bing Wu
Journal: Journal of Hazardous Materials
Year: 2017
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6)Title: Microbial diversity of the hypersaline and lithium-rich Salar de Uyuni, Bolivia
Author: Götz Haferburg, Janosch A.D. Gröning, Nadja Schmidt, Nicolai-Alexeji Kummer, Juan Carlos Erquicia, Michael Schlömann
Journal: Microbiological Research
Year: 2017
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7)Title: Retrospective mining of toxicology data to discover multispecies and chemical class effects: Anemia as a case study
Author: Richard S. Judson, Matt Martin, Grace Patlewicz, Charles E. Wood
Journal: Regulatory Toxicology and Pharmacology
Year: 2017
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8)Title: Shifts in microbial community structure and function in surface waters impacted by unconventional oil and gas wastewater revealed by metagenomics
Author: N.L. Fahrenfeld, Hannah Delos Reyes, Alessia Eramo, Denise M. Akob, Adam C. Mumford, Isabelle M. Cozzarelli
Journal: Science of The Total Environment
Year: 2017
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9)Title: Study of microbial community plasticity for anaerobic digestion of vegetable waste in Anaerobic Baffled Reactor
Author: Madhuri Gulhane, Prabhakar Pandit, Anshuman Khardenavis, Dharmesh Singh, Hemant Purohit
Journal: Renewable Energy
Year: 2017
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10)Title: Wildfire impact: Natural experiment reveals differential short-term changes in soil microbial communities
Author: Miranda T. Prendergast-Miller, Alexandre B. de Menezes, Lynne M. Macdonald, Peter Toscas, Andrew Bissett, Geoff Baker, Mark Farrell, Alan E. Richardson, Tim Wark, Peter H. Thrall
Journal: Soil Biology and Biochemistry
Year: 2017
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1)Title: Monitoring the microbial community shift throughout the shock changes of hydraulic retention time in an anaerobic moving bed membrane bioreactor
Author: Theint Theint Win, Hyemin Kim, Kangwoo Cho, Kyung Guen Song, Joonhong Park
Journal: Bioresource Technology
Year: 2016
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2)Title: Biotechnological and bioinformatics approaches for augmentation of biohydrogen production: A review
Author: Gopal Ramesh Kumar, Nupoor Chowdhary
Journal: Renewable and Sustainable Energy Reviews
Year: 2016
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3)Title: Bioinformatics aided microbial approach for bioremediation of wastewater containing textile dyes
Author: S. Senthil Kumar, S. Shantkriti, T. Muruganandham, E. Murugesh, Niraj Ranec S.P. Govindwar
Journal: Ecological Informatics
Year: 2016
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4)Title: Enhancing tetrabromobisphenol A biodegradation in river sediment microcosms and understanding the corresponding microbial community
Author: Guiying Lia, Jukun Xiong, Po Keung Wong, Taicheng An
Journal: Environmental Pollution
Year: 2016
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5)Title: Aquatic hyphomycetes in a changing environment
Author: F. Bärlocher
Journal: Fungal Ecology
Year: 2016
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6)Title: A critical review of algal biomass: A versatile platform of bio-based polyesters from renewable resources
Author: Aqdas Noreen, Khalid Mahmood Zia, Mohammad Zuber, Muhammad Ali, Mohammad Mujahid
Journal: International Journal of Biological Macromolecules
Year: 2016
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8)Title: Bioactive hydrolysates from bovine blood globulins: Generation, characterisation, and in silico prediction of toxicity and allergenicity
Author: Tomas Lafarga, Matthias Wilm, Kieran Wynne, Maria Hayes
Journal: Journal of Functional Foods
Year: 2016
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9)Title: Characterization of gene expression profiling of mouse tissues obtained during the postmortem interval
Author: Sayaka Sobue, Keita Sakata, Yuki Sekijima, Shanlou Qiao, Takashi Murate, Masatoshi Ichihara
Journal: Journal of Functional Foods
Year: 2016
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10)Title: Biological characterization of the hygrobafilomycin antibiotic JBIR-100 and bioinformatic insights into the hygrolide family of natural products
Author: Evelyn M. Molloy, Jonathan I. Tietz, Patricia M. Blair, Douglas A. Mitchell
Journal: Bioorganic & Medicinal Chemistry
Year: 2016
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11)Title: Identification and analysis of miRNAs and their targets in ginger using bioinformatics approach
Author: Noopur Singh, Swati Srivastava, Ashok Sharma
Journal: Gene
Year: 2016
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12)Title: Distribution of cold adaptation proteins in microbial mats in Lake Joyce, Antarctica: Analysis of metagenomic data by using two bioinformatics tools
Author: Hyunmin Koo, Joseph A. Hakim, Phillip R.E. Fisher, Alexander Grueneberg, Dale T. Andersen
Journal: Journal of Microbiological Methods
Year: 2016
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13)Title: Bioinformatics tools for lncRNA research
Author: Junichi Iwakiri, Michiaki Hamada, Kiyoshi Asai
Journal: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
Year: 2016
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14)Title: Clinical, genetics and bioinformatics characterization of a campomelic dysplasia case report
Author: Nerea Carvajal, Mónica Martínez-García, Monica Chagoyen, Nieves Morcillo, Ana Pino, I. Lorda, María José Trujillo-Tiebas
Journal: Gene
Year: 2016
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15)Title: Bioinformatics analysis of organizational and expressional characterizations of the IFNs, IRFs and CRFBs in grass carp Ctenopharyngodon idella
Author: Nerea Carvajal, Mónica Martínez-García, Monica Chagoyen, Nieves Morcillo, Ana Pino, I. Lorda, María José Trujillo-Tiebas
Journal: Gene
Year: 2016
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16)Title: Ready to use bioinformatics analysis as a tool to predict immobilisation strategies for protein direct electron transfer (DET)
Author: R. Cazelles, N. Lalaoui, T. Hartmann, S. Leimkühler, U. Wollenberger, M. Antonietti, S. Cosnier
Journal: Biosensors and Bioelectronics
Year: 2016
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17)Title: Identification of microRNAs correlated with citrus granulation based on bioinformatics and molecular biology analysis
Author: Jing Zhang, Miao Wang, Fansheng Cheng, Chao Dai, Yufeng Sun, Jia Lu, Yatao Huang, Minmin Li, Yan He, Fengzhong Wang, Bei Fan
Journal: Postharvest Biology and Technology
Year: 2016
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18)Title: Regulatory bioinformatics for food and drug safety
Author: Marion J. Healy, Weida Tong, Stephen Ostroff, Hans-Georg Eichler, Alex Patak, Margaret Neuspiel, Hubert Deluyker, William Slikker
Journal: Regulatory Toxicology and Pharmacology
Year: 2016
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19)Title: Making sense of genomes of parasitic worms: Tackling bioinformatic challenges
Author: Pasi K. Korhonen, Neil D. Young, Robin B. Gasser
Journal: Biotechnology Advances
Year: 2016
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20)Title: Metagenomics as a preliminary screen for antimicrobial bioprospecting
Author: Pasi K. Korhonen, Neil D. Young, Robin B. Gasser
Journal: Gene
Year: 2016
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21)Title: Aquatic hyphomycetes in a changing environment
Author: F. Bärlocher
Journal: Fungal Ecology
Year: 2016
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22)Title: Efficiency of different solarization-based ecological soil treatments on the control of Fusarium wilt and their impacts on the soil microbial community
Author: Yanlai Yao, Zhiyong Xue, Chunlai Hong, FengXiang Zhu, Xiaoyang Chen, Weiping Wang, Zucong Cai, Nan Huang, Xinqin Yang
Journal: Applied Soil Ecology
Year: 2016
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23)Title: The effect of different carbon sources on the nutritional composition, microbial community and structure of bioflocs
Author: YanFang Wei, Shao-An Liao, An-li Wang
Journal: Aquaculture
Year: 2016
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24)Title: Performance of a full-scale modified anaerobic/anoxic/oxic process: High-throughput sequence analysis of its microbial structures and their community functions
Author: Yasong Chen, Zheng Zhao, Yuke Peng, Jie Li, Lin Xiao, Liuyan Yang
Journal: Bioresource Technology
Year: 2016
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25)Title: Correlating microbial community profiles with geochemical conditions in a watershed heavily contaminated by an antimony tailing pond ?
Author: Enzong Xiao, Valdis Krumins, Song Tang, Tangfu Xiao, Zengping Ning, Xiaolong Lan, Weimin Sun
Journal: Environmental Pollution
Year: 2016
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26)Title: Soil biochar amendment shapes the composition of N2O-reducing microbial communities
Author: Johannes Harter, Pascal Weigold, Mohamed El-Hadidi, Daniel H. Huson, Andreas Kappler, Sebastian Behrens
Journal: Science of The Total Environment
Year: 2016
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27)Title: How do microbial communities in top- and subsoil respond to root litter addition under field conditions?
Author: Muhammad Sanaullah, Abad Chabbi, Pierre-Alain Maron, Karen Baumann, Vincent Tardy, Evgenia Blagodatskaya, Yakov Kuzyakov, Cornelia Rumpel
Journal: Soil Biology and Biochemistry
Year: 2016
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28)Title: Soil microbial communities as potential regulators of in situ N2O fluxes in annual and perennial cropping systems
Author: K.A. Thompson, E. Bent, D. Abalos, C. Wagner-Riddle, K.E. Dunfield
Journal: Soil Biology and Biochemistry
Year: 2016
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29)Title: Metagenomics: Probing pollutant fate in natural and engineered ecosystems
Author: Emna Bouhajja, Spiros N. Agathos, Isabelle F. George
Journal: Biotechnology Advances
Year: 2016
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30)Title: Oil sands tailings ponds harbour a small core prokaryotic microbiome and diverse accessory communities
Author: S.L. Wilson, C. Li, E. Ramos-Padrón, C. Nesbø, J. Soh, C.W. Sensen, G. Voordouw, J. Foght, L.M. Gieg
Journal: Journal of Biotechnology
Year: 2016
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1)Title: Application of bioinformatics tools and databases in microbial dehalogenation research: A review
Author: R. Satpathy, V. B. Konkimalla, J. Ratha
Journal: Applied Biochemistry and Microbiology
Year: 2015
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2)Title: Normalization of environmental metagenomic DNA enhances the discovery of under-represented microbial community members
Author: J.-B. Ramond, T.P. Makhalanyane, M.I. Tuffin, D.A. Cowan
Journal: Letters in Applied Microbiology
Year: 2015
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3)Title: Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology
Author: Molly K Gibson, Kevin J Forsberg, Gautam Dantas
Journal: The ISME Journal
Year: 2015
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4)Title: The Integrated Microbial Genome Resource of Analysis
Author: Alice Checcucci, Alessio Mengoni
Journal: Bacterial Pangenomics
Year: 2015
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5)Title: Environmental Metagenomics: The Data Assembly and Data Analysis Perspectives
Author: Vinay Kumar, S. S. Maitra, Rohit Nandan Shukla
Journal: Journal of The Institution of Engineers
Year: 2015
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6)Title: Transcriptome analysis of Escherichia coli O157:H7 grown in vitro in the sterile-filtrated cecal content of human gut microbiota associated rats reveals an adaptive expression of metabolic and virulence genes
Author: Guillaume Le Bihan, Grégory Jubelin, Philippe Garneau, Annick Bernalier-Donadille, Christine Martin, Francis Beaudry, Josée Harel
Journal: Microbes and Infection
Year: 2015
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7)Title: Proteotyping: Proteomic characterization, classification and identification of microorganisms – A prospectus
Author: Roger Karlsson, Lucia Gonzales-Siles, Fredrik Boulund, Liselott Svensson-Stadler, Susann Skovbjerg, Anders Karlsson, Max Davidson, Stefan Hulth, Erik Kristianssond, Edward R.B. Moore
Journal: Systematic and Applied Microbiology
Year: 2015
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8)Title: Evaluation of Simultaneous Nutrient and COD Removal with Polyhydroxybutyrate (PHB) Accumulation Using Mixed Microbial Consortia under Anoxic Condition and Their Bioinformatics Analysis
Author: Jyotsnarani Jena, Ravindra Kumar, Anshuman Dixit, Sony Pandey, Trupti Das
Journal: PLoS
Year: 2015
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9)Title: Activity and phylogenetic diversity of sulfate-reducing microorganisms in low-temperature subsurface fluids within the upper oceanic crust
Author: Alberto Robador, Sean P. Jungbluth, Douglas E. LaRowe, Robert M. Bowers, Michael S. Rappé, Jan P. Amend and James P. Cowen
Journal: Frontiers in Microbiology
Year: 2015
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10)Title: Possible Biomarkers for the Early Detection of HIV-associated Heart Diseases: A Proteomics and Bioinformatics Prediction
Author: Suraiya Rasheed, Rahim Hashim, Jasper S. Yan
Journal: Computational and Structural Biotechnology Journal
Year: 2015
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11)Title: In Silico Approach to Study the Regulatory Mechanisms and Pathways of Microorganisms
Author: Arun Vairagi
Journal: Applied Environmental Biotechnology: Present Scenario and Future Trends
Year: 2015
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12)Title: In-silico prediction of drug targets, biological activities, signal pathways and regulating networks of dioscin based on bioinformatics
Author: Lianhong Yin, Lingli Zheng, Lina Xu, Deshi Dong, Xu Han, Yan Qi, Yanyan Zhao, Youwei Xu and Jinyong Peng
Journal: BMC Complementary and Alternative Medicine
Year: 2015
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13)Title: Functional Genomics, Genetics, and Bioinformatics
Author: Youping Deng, Hongwei Wang, Ryuji Hamamoto, David Schaffer, and Shiwei Duan
Journal: BioMed Research International
Year: 2015
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14)Title: Nonproteinogenic D-Amino Acids at Millimolar Concentrations Are a Toxin for Anaerobic Microorganisms Relevant to Early Earth and Other Anoxic Planets
Author: Sophie L. Nixon and Charles S. Cockell
Journal: Astrobiology
Year: 2015
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15)Title: Identification of a novel carbohydrate esterase from Bjerkandera adusta: Structural and function predictions through bioinformatics analysis and molecular modeling
Author: Laura I. Cuervo-Soto, Gilberto Valdés-García, Ramón Batista-García, María del Rayo Sánchez-Carbente, Edgar Balcázar-López, Verónica Lira-Ruan, Nina Pastor and Jorge Luis Folch-Mallol
Journal: Proteins: Structure, Function, and Bioinformatics
Year: 2015
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16)Title: Physiological and evolutionary potential of microorganisms from the Canterbury Basin subseafloor, a metagenomic approach
Author: Frédéric Gaboyer , Gaëtan Burgaud , Karine Alain
Journal: FEMS Microbiology Ecology
Year: 2015
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17)Title: The effects of biochar and compost amendments on copper immobilization and soil microorganisms in a temperate vineyard
Author: K.A. Mackie, S. Marhan, F. Ditterich, H.P. Schmidt, E. Kandeler
Journal: Agriculture, Ecosystems & Environment
Year: 2015
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18)Title: Higher diversity and abundance of denitrifying microorganisms in environments than considered previously
Author: Wei Wei, Kazuo Isobe, Tomoyasu Nishizawa, Lin Zhu, Yutaka Shiratori, Nobuhito Ohte, Keisuke Koba, Shigeto Otsuka and Keishi Senoo
Journal: The ISME Journal
Year: 2015
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19)Title: Developing expertise in bioinformatics for biomedical research in Africa
Author: Thomas K. Karikari, Emmanuel Quansah, Wael M.Y. Mohamed
Journal: Applied & Translational Genomics
Year: 2015
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20)Title: Widening participation would be key in enhancing bioinformatics and genomics research in Africa
Author: Thomas K. Karikari, Emmanuel Quansah, Wael M.Y. Mohamed
Journal: Applied & Translational Genomics
Year: 2015
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21)Title: Neurogenomics: An opportunity to integrate neuroscience, genomics and bioinformatics research in Africa
Author: Thomas K. Karikari, Jelena Aleksic
Journal: Applied & Translational Genomics
Year: 2015
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22)Title: Bioinformatics in protein kinases regulatory network and drug discovery
Author: Qingfeng Chen, Haiqiong Luoc, Chengqi Zhangd, Yi-Ping Phoebe Chen
Journal: Mathematical Biosciences
Year: 2015
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23)Title: Bioinformatics analysis of gene expression profiles of osteoarthritis
Author: Qiang Wang, Yufei Li, Zhiqiang Zhang, Yongchao Fang, Xiaolei Li, Yu Sun, Chuanzhi Xiong, Lianqi Yan, Jianning Zhao
Journal: Acta Histochemica
Year: 2015
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24)Title: Analysis of Parkinson's disease pathophysiology using an integrated genomics-bioinformatics approach
Author: Li M. Fu, Katherine A. Fu
Journal: Pathophysiology
Year: 2015
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25)Title: Distribution of cold adaptation proteins in microbial mats in Lake Joyce, Antarctica: Analysis of metagenomic data by using two bioinformatics tools
Author: Hyunmin Koo, Joseph A. Hakim, Phillip R.E. Fisher, Alexander Gruneberg, Dale T. Andersen
Journal: Journal of Microbiological Methods
Year: 2015
View Abstract | Full Paper Request 

26)Title: Bioinformatics prioritization of SNPs perturbing microRNA regulation of hematological malignancy-implicated genes
Author: Hamid Ghaedi, Milad Bastami, Davood Zare-Abdollahi, Behnam Alipoor, Abolfazl Movafagh, Reza Mirfakhraie, Mir Davood Omrani, Andrea Masotti
Journal: Genomics
Year: 2015
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27)Title: In search of key genes associated with endometriosis using bioinformatics approach
Author: Fangmei Liu, Xiaomei Lv, Haifeng Yu, Ping Xu, Rong Ma, Kun Zou
Journal: European Journal of Obstetrics & Gynecology and Reproductive Biology
Year: 2015
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28)Title: Identification of novel and differentially expressed microRNAs in ovine ovary and testis tissues using Solexa sequencing and bioinformatics
Author: Wei-hua CHANG, Yong ZHANG, Zhang-rui CHENG, Xing-xu ZHAO, Juan-hong WANG, You-ji MA, Jun-jie HU, Quan-wei ZHANG
Journal: Journal of Integrative Agriculture
Year: 2015
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29)Title: Mining for sensitive and reliable species-specific primers for PCR for detection of Cronobacter sakazakii by a bioinformatics approach
Author: Chen Qiming, Tao Tingting, Bie Xiaomei, Lu Yingjian†, Lu Fengxia, Zhai Ligong, Lu Zhaoxin
Journal: Journal of Dairy Science
Year: 2015
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30)Title: Using combinatorial bioinformatics methods to analyze annual perspective changes of influenza viruses and to accelerate development of effective vaccines
Author: Yu-Jen Hu, Kuan-Chih Chow, Ching-Chuan Liu, Li-Jen Lin, Sheng-Cheng Wang, Shulhn-Der Wang
Journal: Journal of the Formosan Medical Association
Year: 2015
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31)Title: Application of bioinformatics in probe design enables detection of enteroviruses on different taxonomic levels by advanced in situ hybridization technology
Author: Jutta E. Laiho, Sami Oikarinen, Maarit Oikarinen, Pär G. Larsson, Virginia M. Stone, Didier Hober, Steven Oberste, Malin Flodström-Tullberg, Jorma Isola, Heikki Hyöty
Journal: Journal of Clinical Virology
Year: 2015
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32)Title: Lectin genes and their mature proteins: Still an exciting matter, as revealed by biochemistry and bioinformatics analyses of newly reported proteins
Author: Andreia Varmes Fernandes, Márcio Viana Ramos, José Hélio Costa, Ilka Maria Vasconcelos, Renato de Azevedo Moreira, Frederico Bruno Mendes Batista Moreno, Maria Eliza Caldas dos Santos, José Francisco de Carvalho Gonçalves
Journal: Biochemical Systematics and Ecology
Year: 2015
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33)Title: Identification of a Human Papillomavirus–Associated Oncogenic miRNA Panel in Human Oropharyngeal Squamous Cell Carcinoma Validated by Bioinformatics Analysis of The Cancer Genome Atlas
Author: Daniel L. Miller, J. Wade Davis, Kristen H. Taylor, Jeff Johnson, Zonggao Shi, Russell Williams, Ulus Atasoy, James S. Lewis Jr., M. Sharon Stack
Journal: The American Journal of Pathology
Year: 2015
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34)Title: MicroRNA expression profiling and bioinformatics analysis of dysregulated microRNAs in vinorelbine-resistant breast cancer cells
Author: Shanliang Zhong, Tengfei Ma, Xiaohui Zhang, Mengmeng Lv, Lin Chen, Jinhai Tang, Jianhua Zhao
Journal: Gene
Year: 2015
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35)Title: Bioinformatic analysis of a PLP-dependent enzyme superfamily suitable for biocatalytic applications
Author: Fabian Steffen-Munsberg, Clare Vickers, Hannes Kohls, Henrik Land, Hendrik Mallin, Alberto Nobili, Lilly Skalden, Tom van den Bergh, Henk-Jan Joosten, Per Berglund, Matthias Höhne, Uwe T. Bornscheuer
Journal: Biotechnology Advances
Year: 2015
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36)Title: Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires
Author: Victor Greiff, Enkelejda Miho, Ulrike Menzel, Sai T. Reddy
Journal: Trends in Immunology
Year: 2015
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37)Title: Bioinformatic identification of cytochrome b5 homologues from the parasitic nematode ascaris suum and the free-living nematode Caenorhabditis elegans highlights the crucial role of A. suum adult-specific secretory cytochrome b5 in parasitic adaptation
Author: Shinzaburo Takamiya, Muneaki Hashimoto, Toshihiro Mita, Takehiro Yokota, Yoshitaka Nakajima, Fumiyuki Yamakura, Shigetoshi Sugio, Tsutomu Fujimura, Takashi Ueno, Hiroshi Yamasaki
Journal: Parasitology International
Year: 2015
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38)Title: A bioinformatic approach to check the spatial epitope structure of an immunogenic protein coded by DNA vaccine plasmids
Author: M. Ghaemi Bafghi, M.R. Bassami, Gh.R. Hashemi Tabar, M.R. Saberi, A.R. Haghparast, H. Dehghani
Journal: Journal of Theoretical Biology
Year: 2015
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39)Title: Next-generation re-sequencing as a tool for rapid bioinformatic screening of presence and absence of genes and accessory chromosomes across isolates of Zymoseptoria tritici
Author: Megan C. McDonald, Angela H. Williams, Andrew Milgate, Julie A. Pattemore, Peter S. Solomon, James K. Hane
Journal: Fungal Genetics and Biology
Year: 2015
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40)Title: The Screening of Genes Sensitive to Long-Term, Low-Level Microwave Exposure and Bioinformatic Analysis of Potential Correlations to Learning and Memory
Author: Ya Li ZHAO, Ying Xian LI, Hong Bo MA, Dong LI, Hai Liang LI, Rui JIANG, Guang Han KAN, Zhen Zhong YANG, Zeng Xin HUANG 
Journal: Biomedical and Environmental Sciences
Year: 2015
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41)Title: Bioinformatic analysis of neurotropic HIV envelope sequences identifies polymorphisms in the gp120 bridging sheet that increase macrophage-tropism through enhanced interactions with CCR5
Author: Megan E. Mefford, Kevin Kunstman, Steven M. Wolinsky, Dana Gabuzda
Journal: Virology
Year: 2015
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42)Title: Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics
Author: Matthias Farlik, Nathan C. Sheffield, Angelo Nuzzo, Paul Datlinger, Andreas Schönegger, Johanna Klughammer, Christoph Bock
Journal: Cell Reports
Year: 2015
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43)Title: Soil and Rhizosphere Associated Fungi in Grey Mangroves (Avicennia marina) from the Red Sea — A Metagenomic Approach
Author: Marta Filipa Simões, André Antunes, Cristiane A. Ottoni, Mohammad Shoaib Amini, Intikhab Alam, Hanin Alzubaidy, Noor-Azlin Mokhtar, John A.C. Archer, Vladimir B. Bajic
Journal: Genomics, Proteomics & Bioinformatics
Year: 2015
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1)Title: A Taxonomic Signature of Obesity in the Microbiome? Getting to the Guts of the Matter
Author: Mariel M. Finucane, Thomas J. Sharpton, Timothy J. Laurent, Katherine S. Pollard mail
Journal: PLoS ONE
Year: 2014
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2)Title: Bioinformatics Resources for the Management of Biological Information on Plant Responses Towards Stresses
Author: Ratna Prabha, Dhananjaya P. Singh, Vivek Keshri, Sevyaa, Arun K. Sharma
Journal: Biology of useful plants and microbes
Year: 2014
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3)Title: Does urbanization shape bacterial community composition in urban park soils? A case study in 16 representative Chinese cities based on the pyrosequencing method
Author: Hui-Juan Xu, Shun Li, Jian-Qiang Su, San'an Nie, Valerie Gibson, Hu Li, Yong-Guan Zhu
Journal: FEMS Microbiology Ecology
Year: 2014
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4)Title: Draft Genome Sequence of Brevibacillus panacihumi Strain W25, a Halotolerant Hydrocarbon-Degrading Bacterium
Author: Xinxin Wang, Decai Jin, Lisha Zhou, Liang Wu, Wei An, Yu Chen, Lin Zhao
Journal: Genome Announc
Year: 2014
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5)Title: Gene-environment interaction between SCN5A-1103Y and hypokalemia influences QT interval prolongation in African Americans: The Jackson Heart Study
Author: Ermeg L. Akylbekova, PhD, John P. Payne, MD, Christopher Newton-Cheh, MD, Warren L. May, PhD, Ervin R. Fox, MD, James G. Wilson, MD, Daniel F. Sarpong, PhD, Herman A. Taylor, MD, Joseph F. Maher, MD
Journal: American Heart Journal
Year: 2014
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6)Title: Lateral transfer of eukaryotic ribosomal RNA genes: an emerging concern for molecular ecology of microbial eukaryotes
Author: Akinori Yabuki, Takashi Toyofuku and Kiyotaka Takishita
Journal: The ISME Journal
Year: 2014
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7)Title: Metabolomic analysis of soil communities can be used for pollution assessment
Author: Oliver A.H. Jones, Stephanie Sdepanian, Steven Lofts, Claus Svendsen, David J. Spurgeon, Mahon L. Maguire, Julian L. Griffin
Journal: Environmental Toxicology and Chemistry
Year: 2014
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8)Title: Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California
Author: Erik R. Hawley, , Hailan Piao, Nicole M. Scott, Stephanie Malfatti, Ioanna Pagani, Marcel , Huntemann, Amy Chen, Tijana Glavina del Rio, Brian Foster, Alex Copeland, Janet Jansson, Amrita Pati, Susannah Tringe, Jack A. Gilbert, Thomas D. Lorenson, Matthias Hess
Journal: Standards in Genomic Sciences
Year: 2014
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9)Title: Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity
Author: Fan Lü, Ariane Bize, Alain Guillot, Véronique Monnet, Céline Madigou, Olivier Chapleur, Laurent Mazéas, Pinjing He and Théodore Bouchez
Journal: The ISME Journal
Year: 2014
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10)Title: Microbial Enhanced Heavy Oil Recovery by the Aid of Inhabitant Spore-Forming Bacteria: An Insight Review
Author: Biji Shibulal, Saif N. Al-Bahry, Yahya M. Al-Wahaibi, Abdulkader E. Elshafie, Ali S. Al-Bemani, and Sanket J. Joshi
Journal: The Scientific World Journal
Year: 2014
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11)Title: Microbial leaching of metals from solid industrial wastes
Author: Debaraj Mishra, Young Ha Rhee
Journal: Journal of Microbiology
Year: 2014
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12)Title: PATRIC, the bacterial bioinformatics database and analysis resource
Author: Alice R. Wattam, David Abraham, Oral Dalay, Terry L. Disz,Timothy Driscoll, Joseph L. Gabbard, Joseph J. Gillespie, Roger Gough,Deborah Hix, Ronald Kenyon, Dustin Machi, Chunhong Mao, Eric K. Nordberg, Robert Olson, Ross Overbeek, Gordon D. Pusch, Maulik Shukla, Julie Schulman, Rick L. Stevens, Daniel E. Sullivan, Veronika Vonstein, Andrew Warren, Rebecca Will, Meredith J.C. Wilson, Hyun Seung Yoo,Chengdong Zhang, Yan Zhang and Bruno W. Sobral
Journal: Nucleic Acids Research
Year: 2014
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13)Title: Productivity and influence in bioinformatics: A bibliometric analysis using PubMed central
Author: Min Song, SuYeon Kim, Guo Zhang,Ying Ding, Tamy Chambers
Journal: Journal of the Association for Information Science and Technology
Year: 2014
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14)Title: Role of cloud computing in bioinformatics research for handling the huge biological data
Author: Radhe Shyam Thakur and Rajib Bandopadhyay
Journal: Biology of useful plants and microbes
Year: 2014
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15)Title: The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
Author: Ross Overbeek, Robert Olson, Gordon D. Pusch, Gary J. Olsen,James J. Davis, Terry Disz, Robert A. Edwards, Svetlana Gerdes,Bruce Parrello, Maulik Shukla, Veronika Vonstein, Alice R. Wattam,Fangfang Xia and Rick Stevens
Journal: Nucleic Acids Research
Year: 2014
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16)Title: Translational Bioinformatics and Clinical Research Informatics
Author: C. Daniel, E. Albuisson, T. Dart, P. Avillach, M. Cuggia, Y. Guo
Journal: Medical Informatics
Year: 2014
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17)Title: A bioinformatics approach to the determination of genes involved in endophytic behavior in Burkholderia spp.
Author: Shimaila Ali, Jin Duan, Trevor C. Charles, Bernard R. Glick
Journal: Journal of Industrial Microbiology & Biotechnology
Year: 2014
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18)Title: Extracting data from the muck: deriving biological insight from complex microbial communities and non-model organisms with next generation sequencing
Author: Kevin V Solomon, Charles H Haitjema, Dawn A Thompson, Michelle A O’Malley
Journal: Current Opinion in Biotechnology
Year: 2014
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19)Title: MetaRef: a pan-genomic database for comparative and community microbial genomics
Author: Katherine Huang, Arthur Brady, Anup Mahurkar, Owen White, Dirk Gevers, Curtis Huttenhower and Nicola Segata
Journal: Nucleic Acids Research
Year: 2014
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20)Title: Microbial genome mining for accelerated natural products discovery: is a renaissance in the making?
Author: Brian O. Bachmann, Steven G. Van Lanen, Richard H. Baltz
Journal: Journal of Industrial Microbiology & Biotechnology
Year: 2014
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21)Title: Mining locus tags in PubMed Central to improve microbial gene annotation
Author: Chris J Stubben and Jean F Challacombe
Journal: BMC Bioinformatics
Year: 2014
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22)Title: RefSeq microbial genomes database: new representation and annotation strategy
Author: Tatiana Tatusova, Stacy Ciufo, Boris Fedorov, Kathleen O’Neill and Igor Tolstoy
Journal: Nucleic Acids Research
Year: 2014
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23)Title: VAMPS: a website for visualization and analysis of microbial population structures
Author: Susan M Huse, David B Mark Welch, Andy Voorhis, Anna Shipunova, Hilary G Morrison, A Murat Eren and Mitchell L Sogin
Journal: BMC Bioinformatics
Year: 2014
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24)Title: Bioinformatic Approaches Reveal Metagenomic Characterization of Soil Microbial Community
Author: Zhuofei Xu, Martin Asser Hansen, Lars H. Hansen, Samuel Jacquiod, Søren J. Sørensen
Journal: PLoS ONE
Year: 2014
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25)Title: Comparative functional genomics of Lactobacillusspp. reveals possible mechanisms for specialization of vaginal lactobacilli to their environment
Author: Helena Mendes-Soares, Haruo Suzuki, Roxana J. Hickey and Larry J. Forney
Journal: Journal of bacteriology
Year: 2014
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26)Title: Soil Microbial Responses to Increased Moisture and Organic Resources along a Salinity Gradient in a Polar Desert
Author: David J. Van Horn, Jordan G. Okie, Heather N. Buelow, Michael N. Gooseff, John E. Barrett and Cristina D. Takacs-Vesbach
Journal: Appl. Environ. Microbio
Year: 2014
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27)Title: The Bio-Community Perl toolkit for microbial ecology
Author: Florent E. Angly, Christopher J. Fields and Gene W. Tyson
Journal: BMC Bioinformatics
Year: 2014
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28)Title: The unseen world: environmental microbial sequencing and identification methods for ecologists
Author: Naupaka Zimmerman , Jacques Izard , Christian Klatt, Jizhong Zhou, Emma Aronson
Journal: Frontiers in Ecology and the Environment
Year: 2014
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29)Title: Microbial Metabolic Potential for Carbon Degradation and Nutrient (Nitrogen and Phosphorus) Acquisition in an Ombrotrophic Peatland
Author: Xueju Lin, Malak M. Tfaily, Stefan J. Green, J. Megan Steinweg, Patrick Chanton, Aopeau Imvittaya, Jeffrey P. Chanton, William Cooper, Christopher Schadt, Joel E. Kostka
Journal: Appl. Environ. Microbiol
Year: 2014
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30)Title: Comparative Metagenomic Analysis of Human Gut Microbiome Composition Using Two Different Bioinformatic Pipelines
Author: Pankaj Kumar Arora, Hanhong Bae
Journal: BioMed Research International
Year: 2014
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31)Title: A Novel Bioinformatics Method for Efficient Knowledge Discovery by BLSOM from Big Genomic Sequence Data
Author: Yu Bai, Yuki Iwasaki, Shigehiko Kanaya, Yue Zhao, Toshimichi Ikemura
Journal: BioMed Research International
Year: 2014
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32)Title: Identifying microbes from environmental water samples in a discovery-based learning module
Author: Wenfa Ng
Journal: PeerJ PrePrints
Year: 2014
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33)Title: Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead
Author: Simon Joly,T. Jonathan Davies, Annie Archambault, Anne Bruneau, Alison Derry, Steven W. Kembel5, Pedro Peres-Neto, Jana Vamosi, Terry A. Wheeler
Journal: Molecular Ecology Resources
Year: 2014
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34)Title: Metagenomic analysis reveals microbial diversity and function in the rhizosphere soil of a constructed wetland
Author: Yaohui Bai, Jinsong Liang, Ruiping Liu, Chengzhi Hu & Jiuhui Qu
Journal: Environmental Technology
Year: 2014
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35)Title: Brazilian Microbiome Project: Revealing the Unexplored Microbial Diversity—Challenges and Prospects
Author: Marcos Rogério Tótola, Penny Ruth Hirsch, Alexandre Soares Rosado, Aristóteles Góes-Neto, Artur Luiz da Costa da Silva, Carlos Augusto Rosa, Daniel Kumazawa Morais, Fernando Dini Andreote, Gabriela Frois Duarte, Itamar Soares de Melo, Lucy Seldin, Márcio Rodrigues Lambais, Mariangela Hungria, Raquel Silva Peixoto, Ricardo Henrique Kruger, Siu Mui Tsai, Vasco Azevedo
Journal: Microbial Ecology
Year: 2014
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36)Title: Integration of bioinformatics to biodegradation
Author: Pankaj Kumar Arora, Hanhong Bae
Journal: Arora and Bae Biological Procedures
Year: 2014
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37)Title: Bioinformatics for precision medicine in oncology: principles and application to the SHIVA clinical trial
Author: Nicolas Servant, Julien Roméjon, Pierre Gestraud, Philippe La Rosa, Georges Lucotte, Séverine Lair, Virginie Bernard, Bruno Zeitouni, Fanny Coffin, Gérôme Jules-Clément, Florent Yvon, Alban Lermine, Patrick Poullet, Stéphane Liva, Stuart Pook, Tatiana Popova, Camille Barette, François Prud’homme, Jean-Gabriel Dick, Maud Kamal,8 Christophe Le Tourneau, Emmanuel Barillot, Philippe Hupé
Journal: Front Genet
Year: 2014
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38)Title: Using Kepler for Tool Integration in Microarray Analysis Workflows
Author: Zhuohui Gan , Jennifer C. Stowe, Ilkay Altintas, Andrew D. McCulloch, Alexander C. Zambon
Journal: Procedia Computer Science
Year: 2014
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39)Title: RNA-Seq Analysis Pipeline Based on Oshell Environment
Author: Jing Li., Jun Hu, Newman, M., Kejun Liu
Journal: Computational Biology and Bioinformatics
Year: 2014
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40)Title: Coordination characterization of zinc metalloproteins
Author: Sen Yao, Robert M Flight, Hunter NB Moseley
Journal: BMC Bioinformatics
Year: 2014
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41)Title: Bioinfo-Kit: A Sharing Software Tool for Bioinformatics
Author: Yu Huang, Jian Yong Wang, Xiao Mei Wei, Bin Hu
Journal: Applied Mechanics and Materials
Year: 2014
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42)Title: Bioinformatics analysis of bacteriophage and prophage endolysin domains
Author: Barbora Vidová, Zuzana Šramková, Lenka Tišáková, Michaela Oravkinová, Andrej Godány
Journal: Concurrency and Computation: Practice and Experience
Year: 2014
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43)Title: Spectrophotometric Determination of Al(III) in Environment Water with p-Carboxyarsenazo
Author: Lin Gao, Bo Yan, Fang Chen, Jun Long Yao
Journal: Advanced Materials Research
Year: 2014
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44)Title: Physical, policy, and sociocultural characteristics of the primary school environment are positively associated with children's physical activity during class time
Author: Martin K, Bremner A, Salmon J, Rosenberg M, Giles-Corti B
Journal: Journal of Physical Activity & Health
Year: 2014
View Abstract | Full Paper Request 

_____________________________________________________________________________________________________________________

1)Title: Biofuels as a sustainable energy source: An update of the applications of proteomics in bioenergy crops and algae
Author: Bongani Kaiser Ndimba, Roya Janeen Ndimba, T. Sudhakar Johnson, Rungaroon Waditee-Sirisattha, Masato Baba, Sophon Sirisattha, Yoshihiro Shiraiwa, Ganesh Kumar Agrawal, Randeep Rakwal
Journal: Journal of Proteomics
Year: 2013
View Abstract | Full Paper Request

2)Title: Bioinformatics tools for secretome analysis
Author: Dario Caccia, Matteo Dugo, Maurizio Callari, Italia Bongarzone
Journal: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
Year: 2013
View Abstract | Full Paper Request

3)Title: Elucidating the fungal stress response by proteomics
Author: Kristin Kroll, Vera Pähtz, Olaf Kniemeyer
Journal: Journal of Proteomics
Year: 2013
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4)Title: Exploring the potential of applying proteomics for tracking bisphenol A and nonylphenol degradation in activated sludge
Author: Neus Collado, Gianluigi Buttiglieri, Boris A. Kolvenbach, Joaquim Comas, Philippe F.-X. Corvini, Ignasi Rodríguez-Roda
Journal: Chemosphere
Year: 2013
View Abstract | Full Paper Request

5)Title: Genomics in marine monitoring: New opportunities for assessing marine health status
Author: Sarah J. Bourlat, , Angel Borja, Jack Gilbert, Martin I. Taylor, Neil Davies, Stephen B. Weisberg, John F. Griffith, Teresa Lettieri, Dawn Field, John Benzie, Frank Oliver Glöckner, Naiara Rodríguez-Ezpeleta, Daniel P. Faith, Tim P. Bean, Matthias Obst
Journal: Marine Pollution Bulletin
Year: 2013
View Abstract | Full Paper Request

6)Title: Metaproteomics of our microbiome — Developing insight in function and activity in man and model systems
Author: Carolin A. Kolmeder, Willem M. de Vos
Journal: Journal of Proteomics
Year: 2013
View Abstract | Full Paper Request

7)Title: Proteogenomic insights into salt tolerance by a halotolerant alpha-proteobacterium isolated from an Andean saline spring
Author: Carolina Rubiano-Labrador, Céline Bland, Guylaine Miotello, Philippe Guérin, Olivier Pible, Sandra Baena, Jean Armengaud
Journal: Journal of Proteomics
Year: 2013
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8)Title: Proteomic analysis of mycelium and secretome of differentBotrytis cinerea wild-type strains
Author: Raquel González-Fernández, Kerman Aloria, José Valero-Galván, Inmaculada Redondo, Jesús M Arizmendi, Jesús V. Jorrín-Novo
Journal: Journal of Proteomics
Year: 2013
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9)Title: Proteomics and bioinformatics analysis reveal underlying pathways of infection associated histologic chorioamnionitis in pPROM
Author: V. Tambor, M. Kacerovsky, J. Lenco, G. Bhat, R. Menon
Journal: Placenta
Year: 2013
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10)Title: Proteomics approaches for the analysis of enriched microbial subpopulations and visualization of complex functional information
Author: Jörg Bernhardt, Stephan Michalik, Bernd Wollscheid, Uwe Völker, Frank Schmidt
Journal: Current Opinion in Biotechnology
Year: 2013
View Abstract | Full Paper Request

11)Title: Quantitative proteomics reveals dynamic responses ofSynechocystis sp. PCC 6803 to next-generation biofuel butanol
Author: Xiaoxu Tian, Lei Chen, Jiangxin Wang, Jianjun Qiao, Weiwen Zhang
Journal: Journal of Proteomics
Year: 2013
View Abstract | Full Paper Request

12)Title: Searching for microbial protein over-expression in a complex matrix using automated high throughput MS-based proteomics tools
Author: Michiel Akeroyd, Maurien Olsthoorn, Jort Gerritsma, Diana Gutker-Vermaas, Laurens Ekkelkamp, Tjeerd van Rij, Paul Klaassen, Wim Plugge, Ed Smit, Kerstin Strupat, Thibaut Wenzel, Marcel van Tilborg, Rob van der Hoeven
Journal: Journal of Biotechnology
Year: 2013
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13)Title: Subpopulation-proteomics in prokaryotic populations
Author: Michael Jahn, Jana Seifert, Martin von Bergen, Andreas Schmid, Bruno Bühler, Susann Müller
Journal: Current Opinion in Biotechnology
Year: 2013
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14)Title: The characterisation of eukaryotic microbial communities on sandstone buildings in Belfast, UK, using TRFLP and 454 pyrosequencing
Author: Nick A. Cutler, Anna E. Oliver, Heather A. Viles, Samin Ahmad, Andrew S. Whiteley
Journal: International Biodeterioration & Biodegradation
Year: 2013
View Abstract | Full Paper Request

15)Title: Which metaproteome? The impact of protein extraction bias on metaproteomic analyses
Author: Dagmar Hajkova Leary, W. Judson Hervey IV, Jeffrey R. Deschamps, Anne W. Kusterbeck, Gary J. Vora
Journal: Molecular and Cellular Probes
Year: 2013
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____________________________________________________________________________________________________________________

1)Title: Analysis and Prediction of Protein Interaction Network of Ralstonia solanacearum
Author: JIANG Chunlei; ZHAO rui; Lü Lingfeng; QIAO Dairong; CAO Yi
Journal: Chinese Journal of Applied and Environmental Biology
Year: 2012
View Abstract | Full Paper Request

2)Title: Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges
Author: Susanne Schmitt, Peter Tsai, James Bell, Jane Fromont, Micha Ilan, Niels Lindquist, Thierry Perez, Allen Rodrigo, Peter J Schupp, Jean Vacelet, Nicole Webster, Ute Hentschel and Michael W Taylor
Journal: The ISME Journal
Year: 2012
View Abstract | Full Paper Request

3)Title: Bacterial transcription: Transcription factor sliding in live bacteria
Author: Christina Tobin Kåhrström
Journal: Nature Reviews Microbiology
Year: 2012
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4)Title: Bioinformatics analysis of bacterial protective antigens in manually curated Protegen database
Author: Yongqun He, Zuoshuang Xiang
Journal: Procedia in Vaccinology
Year: 2012
View Abstract | Full Paper Request

5)Title: BioNLP Shared Task - The Bacteria Track
Author: Robert Bossy, Julien Jourde, Alain-Pierre Manine, Philippe Veber, Erick Alphonse, Maarten van de Guchte, Philippe Bessières and Claire Nédellec
Journal: BMC Bioinformatics
Year: 2012
View Abstract | Full Paper Request

6)Title: Conversion of viable but nonculturable enteric bacteria to culturable by co-culture with eukaryotic cells
Author: Mitsutoshi Senoh, Jayeeta Ghosh-Banerjee, Thandavarayan Ramamurthy, Rita R. Colwell, Shin-ichi Miyoshi, G. Balakrish Nair, Yoshifumi Takeda
Journal: Microbiology and Immunology
Year: 2012
View Abstract | Full Paper Request

7)Title: De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities
Author: Narasingarao P, Podell S, Ugalde JA, Brochier-Armanet C, Emerson JB, Brocks JJ, Heidelberg KB, Banfield JF, Allen EE
Journal: ISME J.
Year: 2012
View Abstract | Full Paper Request

8)Title:  Diversity of organism in the Usnea longissima lichen
Author: Yunzhe He and Zhiguo Zhang
Journal: African Journal of Microbiology Research
Year: 2012
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9)Title: Diversity, distribution and sources of bacteria in residential kitchens
Author: Gilberto E. Flores, Scott T. Bates, J. Gregory Caporaso, Christian L. Lauber, Jonathan W. Leff, Rob Knight, Noah Fierer
Journal: Environmental Microbiology
Year: 2012
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10)Title: Endosymbiotic bacteria as a source of carotenoids in whiteflies
Author: Daniel B. Sloan and Nancy A. Moran
Journal: Biology Letters
Year: 2012
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11)Title: Eukaryote to gut bacteria transfer of a glycoside hydrolase gene essential for starch breakdown in plants
Author: Maria Cecilia Arias, Étienne G.J. Danchin, Pedro Coutinho, Bernard Henrissat and Steven Ball
Journal: Mobile Genetic Elements Landes Bioscience
Year: 2012
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12)Title: Expression and Bioinformatics Analysis of Pectate Lyase Gene from Bacillus subtilis521
Author: Jing Xiao, Fu-Ping Lu, Yu Li, Jin-Ting Li
Journal: Physics Procedia
Year: 2012
View Abstract | Full Paper Request

13)Title: Fungi and Their Role in Corals and Coral Reef Ecosystems
Author: Chandralata Raghukumar, J. Ravindran
Journal: Progress in Molecular and Subcellular Biology
Year: 2012
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14)Title: Hematodinium sp. and its bacteria-like endosymbiont in European brown shrimp(Crangon crangon)
Author: Grant D Stentiford, Kelly S Bateman, Hamish J Small, Michelle Pond and Anette Ungfors
Journal: Stentiford et al. Aquatic Biosystems
Year: 2012
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15)Title: Horizontal Gene Transfer Between Sclerotinia sclerotiorum and Bacteria
Author: Lü Linfeng; YUE Jianyu; FEI Zhong’an; ZHAO Rui; QIAO Dairong; CAO Yi
Journal: Chinese Journal of Applied and Environmental Biology
Year: 2012
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16)Title: ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria
Author: Dexi Bi, Zhen Xu, Ewan M. Harrison, Cui Tai, Yiqing Wei, Xinyi He, Shiru Jia, Zixin Deng, Kumar Rajakumar and Hong-Yu Ou
Journal: Nucleic Acids Research
Year: 2012
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17)Title: Interfacing medicinal chemistry with structural bioinformatics: implications for T box riboswitch RNA drug discovery
Author: Franziska Jentzsch and Jennifer V Hines
Journal: BMC Bioinformatics
Year: 2012
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18)Title: MALDI TOF MS profiling of bacteria at the strain level: A review
Author: Todd R. Sandrin, Jason E. Goldstein, Stephanie Schumaker
Journal: Mass Spectrometry Reviews
Year: 2012
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19)Title: MALDI-TOF MS Andromas strategy for the routine identification of bacteria, mycobacteria, yeasts, Aspergillus spp. and positive blood cultures
Author: Bille E, Dauphin B, Leto J, Bougnoux ME, Beretti JL, Lotz A, Suarez S, Meyer J, Join-Lambert O, Descamps P, Grall N, Mory F, Dubreuil L, Berche P, Nassif X, Ferroni A
Journal: Clinical Microbiology and Infection
Year: 2012
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20)Title: Nonculture-based identification of bacteria in milk by protein fingerprinting
Author: Juliana Regina Barreiro, Patricia Aparecida Campos Braga, Christina Ramires Ferreira, Markus Kostrzewa, Thomas Maier, Beatrix Wegemann, Viktoria Böettcher, Marcos N. Eberlin, Marcos Veiga dos Santos
Journal: PROTEOMICS
Year: 2012
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21)Title: On the trail of EHEC/EAEC—unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria
Author: Josch Pauling, Richard Röttger, Andreas Neuner, Heladia Salgado, Julio Collado-Vides, Prabhav Kalaghatgi, Vasco Azevedo, Andreas Tauch, Alfred Pühler and Jan Baumbach
Journal: Integrative Biology
Year: 2012
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22)Title: Patho-Genes.org: a website dedicated to gene sequences of potential bioterror bacteria and PCR primers used to amplify them
Author: Julien Gardès, Dipankar Bachar, Olivier Croce, Richard Christen
Journal: Microbial Biotechnology
Year: 2012
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23)Title: Phylogenomics of Prokaryotic Ribosomal Proteins
Author: Natalya Yutin, Pere Puigbò, Eugene V. Koonin, Yuri I. Wolf
Journal: PLoS ONE
Year: 2012
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24)Title: Population Genomics of Early Events in the Ecological Differentiation of Bacteria
Author: B. Jesse Shapiro, Jonathan Friedman, Otto X. Cordero, Sarah P. Preheim, Sonia C. Timberlake, Gitta Szabó, Martin F. Polz, Eric J. Alm
Journal: Science
Year: 2012
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25)Title: Potential Key Bases of Ribosomal RNA to Kingdom-Specific Spectra of Antibiotic Susceptibility and the Possible Archaeal Origin of Eukaryotes
Author: Qiang Xie, Yanhui Wang, Jinzhong Lin, Yan Qin, Ying Wang, Wenjun Bu
Journal: PLoS ONE
Year: 2012
View Abstract | Full Paper Request

26)Title: Predicting sRNAs and Their Targets in Bacteria
Author: Wuju Li, Xiaomin Ying, Qixuan Lu, Linxi Chen
Journal: Genomics, Proteomics and Bioinformatics
Year: 2012
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27)Title: RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics
Author: Pavel S. Novichkov, Thomas S. Brettin, Elena S. Novichkova, Paramvir S. Dehal, Adam P. Arkin, Inna Dubchak and Dmitry A. Rodionov
Journal: Nucleic Acids Research
Year: 2012
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28)Title: sRNAdb: A small non-coding RNA database for gram-positive bacteria
Author: Jordan Pischimarov, Carsten Kuenne, André Billion, Jüergen Hemberger, Franz Cemic, Trinad Chakraborty and Torsten Hain
Journal: BMC Genomics
Year: 2012
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29)Title: Subcellular Localization of Extracytoplasmic Proteins in Monoderm Bacteria: Rational Secretomics-Based Strategy for Genomic and Proteomic Analyses
Author: Sandra Renier, Pierre Micheau, Régine Talon, Michel Hébraud, Mickaël Desvaux
Journal: PLoS ONE
Year: 2012
View Abstract | Full Paper Request

30)Title: Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities
Author: Hikaru Suenaga
Journal: Environmental Microbiology
Year: 2012
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31)Title: Taxonomy of lice and their endosymbiotic bacteria in the post-genomic era
Author: B. M. Boyd, D. L. Reed
Journal: Clinical Microbiology and Infection
Year: 2012
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32)Title: The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens
Author: Kevin J. Forsberg, Alejandro Reyes, Bin Wang, Elizabeth M. Selleck, Morten O. A. Sommer, Gautam Dantas
Journal: Science
Year: 2012
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33)Title: Virus genes in Arctic marine bacteria identified by metagenomic analysis
Author: Matthew T. Cottrell, David L. Kirchman
Journal: AQUATIC MICROBIAL ECOLOGY
Year: 2012
View Abstract | Full Paper Request

________________________________________________________________________________________________________________

1)Title: A NOVEL ANTIBACTERIAL TARGET: PEPTIDE DEFORMYLASE
Author: Sanjay Kumar Verma, R.K. Jat, Narendra Nagar, Rajkumar Saharan, Vineet Sharma, Sanjay pandey, Kuldeep bansal
Journal: Pharmacophore
Year: 2011
View Abstract | Full Paper Request

2)Title: An oxygen reduction chain in the hyperthermophilic anaerobe Thermotoga maritima highlights horizontal gene transfer between Thermococcales and Thermotogales
Author: Le Fourn C, Brasseur G, Brochier-Armanet C, Pieulle L, Brioukhanov A, Ollivier B, Dolla A.
Journal: Environ Microbiol.
Year: 2011
View Abstract | Full Paper Request

3)Title: Comparative bioinformatics analysis of the mammalian and bacterial glycomes
Author: Alexander Adibekian , Pierre Stallforth , Marie-Lyn Hecht , Daniel B. Werz , Pascal Gagneux and Peter H. Seeberger
Journal: Chemical Science
Year: 2011
View Abstract | Full Paper Request

4)Title: Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems
Author: Simon Roux, François Enault, Gisè le Bronner, Didier Debroas
Journal: FEMS Microbiology Ecology
Year: 2011
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5)Title: Emergence and Modular Evolution of a Novel Motility Machinery in Bacteria
Author: Jennifer Luciano, Rym Agrebi, Anne Valérie Le Gall, Morgane Wartel, Francesca Fiegna, Adrien Ducret, Céline Brochier-Armanet, Tâm Mignot
Journal: PLoS Genet
Year: 2011
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6)Title: Genetic diversity of antagonistic endophytic bacteria isolated from Sophora alopecuroide
Author: Lin TianXing; Li Chao; Gong MingFu
Journal: Plant Diseases and Pests
Year: 2011
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7)Title: Genome mining for the discovery of new nitrilases in filamentous fungi
Author: Ondrej Kaplan, Karel Bezouška, Anna Malandra, Alicja B. Veselá, Alena Petrícková, Jürgen Felsberg, Anna Rinágelová, Vladimír Kren, Ludmila Martínková
Journal: Biotechnology Letters
Year: 2011
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8)Title: Genome Sequences of the High-Acetic Acid-Resistant Bacteria Gluconacetobacter europaeus LMG 18890T and G. europaeus LMG 18494 (Reference Strains), G. europaeus 5P3, and Gluconacetobacter oboediens 174Bp2 (Isolated from Vinegar)
Author: Cristina Andrés-Barrao, Laurent Falquet, Sandra P. Calderon-Copete, Patrick Descombes, Ruben Ortega Pérez and François Barja
Journal: Journal of Bacteriology
Year: 2011
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9)Title: Genotype Is a Stronger Determinant than Sex of the Mouse Gut Microbiota
Author: Amir Kovacs, Noa Ben-Jacob, Hanna Tayem, Eran Halperin, Fuad A. Iraqi, Uri Gophna
Journal: Microbial Ecology
Year: 2011
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10)Title: Hidden Fungi, Emergent Properties: Endophytes and Microbiomes
Author: Andrea Porras-Alfaro and Paul Bayman
Journal: Annual Review of Phytopathology
Year: 2011
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11)Title: Membrane RNAs in bacteria
Author: Wes Sanders, Alain Laederach
Journal: Molecular Microbiology
Year: 2011
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12)Title: Meta-analytic approach to the accurate prediction of secreted virulence effectors in gram-negative bacteria
Author: Yoshiharu Sato, Akiko Takaya and Tomoko Yamamoto
Journal: BMC Bioinformatics
Year: 2011
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13)Title: Phylogenetic and genetic variation among Fe(II)-oxidizing acidithiobacilli supports the view that these comprise multiple species with different ferrous iron oxidation pathways
Author: Amouric A, Brochier-Armanet C, Johnson DB, Bonnefoy V, Hallberg KB
Journal: Microbiology
Year: 2011
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14)Title: Regulation of chitinase genes expression in bacteria
Author: Xie CC, Jia HY, Chen YH
Journal: Yi Chuan.
Year: 2011
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15)Title: Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases
Author: Auxilien S, Rasmussen A, Rose S, Brochier-Armanet C, Husson C, Fourmy D, Grosjean H, Douthwaite S
Journal: RNA
Year: 2011
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16)Title: Structure of Hydrogenase in Biohydrogen Production Anaerobic Bacteria
Author: Ming Du, Lu Zhang
Journal: Interdisciplinary Research and Applications in Bioinformatics
Year: 2011
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17)Title: TADB: a web-based resource for Type 2 toxin–antitoxin loci in bacteria and archaea
Author: Yucheng Shao, Ewan M. Harrison, Dexi Bi, Cui Tai, Xinyi He, Hong-Yu Ou, Kumar Rajakumar and Zixin Deng
Journal: Nucleic Acids Research
Year: 2011
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18)Title: The GTPase function of YvcJ and its subcellular relocalization are dependent on growth conditions in Bacillus subtilis
Author: Pompeo F, Luciano J, Brochier-Armanet C, Galinier A
Journal: J Mol Microbiol Biotechnol
Year: 2011
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19)Title: The role of gut microbiota (commensal bacteria) and the mucosal barrier in the pathogenesis of inflammatory and autoimmune diseases and cancer: contribution of germ-free and gnotobiotic animal models of human diseases
Author: Helena Tlaskalová-Hogenová, Renata Štepánková, Hana Kozáková, Tomáš Hudcovic, Luca Vannucci, Ludmila Tucková, Pavel Rossmann, Tomáš Hrncír, Miloslav Kverka, Zuzana Zákostelská, Klára Klimešová, Jaroslava Pribylová, Jirina Bártová, Daniel Sanchez, Petra Fundová, Dana Borovská, Dagmar Šrutková, Zdenek Zídek, Martin Schwarzer, Pavel Drastich and David P Funda
Journal: Cellular and Molecular Immunology
Year: 2011
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____________________________________________________________________________________________________________

1)Title: 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases
Author: Leho Tedersoo, R. Henrik Nilsson, Kessy Abarenkov, Teele Jairus, Ave Sadam, Irja Saar, Mohammad Bahram, Eneke Bechem, George Chuyong, Urmas Kõljalg
Journal: New Phytologist
Year: 2010
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2)Title: A constructive step towards selecting a DNA barcode for fungi
Author: Ursula Eberhardt
Journal: New Phytologist
Year: 2010
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3)Title: An automatic method for identifying surface proteins in bacteria: SLEP
Author: Emanuela Giombini, Massimiliano Orsini, Danilo Carrabino and Anna Tramontano
Journal: BMC Bioinformatics
Year: 2010
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4)Title: An open source chimera checker for the fungal ITS region
Author: R. H. NILSSON, KESSY ABARENKOV, VILMAR VELDRE, STEPHAN NYLINDER, PIERRE DE WIT, SARA BROSCHÉ, JOHAN F. ALFREDSSON, MARTIN RYBERG, ERIK KRISTIANSSON
Journal: Molecular Ecology Resources
Year: 2010
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5)Title: Bioinformatics Computing of Parametric Information Connected with Industrially Important Bacteria
Author: Sant Saran Mishra
Journal: Int. J. Open Problems Compt. Math.
Year: 2010
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6)Title: Characterization and etiology of the bacteria associated with huanglongbing
Author: Teixeira, D. do C.; Wulff, N. A.; Lopes, S. A.; Yamamoto, P. T.; Miranda, M. P. de; Spósito, M. B.; Belasque Júnior, J.; Bassanezi, R. B.
Journal: Citrus Research and Technology
Year: 2010
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7)Title: Characterization and Phylogenetics of a New Species of High Efficient Biohydrogen Production Anaerobic Bacterium
Author: Kun Liu, Yong Feng Li, An Ying Jiao, Xin Yu Pan
Journal: Advanced Materials Research
Year: 2010
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8)Title: Cohorts of arbuscular mycorrhizal fungi (AMF) in Vitis vinifera, a typical Mediterranean fruit crop
Author: Raffaella Balestrini, Franco Magurno, Christopher Walker, Erica Lumini, Valeria Bianciotto
Journal: Environmental Microbiology Reports
Year: 2010
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9)Title: Community dynamics and phylogenetics of bacteria fouling Jet A and JP-8 aviation fuel
Author: L.M. Brown, J.P. McComb, M.D. Vangsness, L.L. Bowen, S.S. Mueller, L.M. Balster, C.A. Bleckmann
Journal: International Biodeterioration and Biodegradation
Year: 2010
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10)Title: Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes
Author: Zasha Weinberg, Joy X Wang, Jarrod Bogue, Jingying Yang, Keith Corbino, Ryan H Moy,Ronald R Breaker
Journal: Genome Biology
Year: 2010
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11)Title: Comparative systems biology: from bacteria to man
Author: Bas Teusink, Hans V. Westerhoff, Frank J. Bruggeman
Journal: Systems Biology and Medicine
Year: 2010
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12)Title: Computational prediction of type III secreted proteins from gram-negative bacteria
Author: Yang Yang, Jiayuan Zhao, Robyn L Morgan, Wenbo Ma and Tao Jiang
Journal: BMC Bioinformatics
Year: 2010
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13)Title: Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA:acetate CoA-transferase gene
Author: Petra Louis, Pauline Young, Grietje Holtrop, Harry J. Flint
Journal: Environmental Microbiology
Year: 2010
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14)Title: Drug discovery from uncultivable microorganisms
Author: Brajesh K. Singh, Catriona A. Macdonald
Journal: Drug Discovery Today
Year: 2010
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15)Title: Faecal indicator bacteria in river biofilms
Author: Balzer M, Witt N, Flemming HC, Wingender J
Journal: Water Science and Technology
Year: 2010
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16)Title: Fluorescence in situ hybridization for molecular cytogenetic analysis in filamentous fungi
Author: Tsuchiya D, Taga M
Journal: Methods in Molecular Biology
Year: 2010
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17)Title: Gene Cloning and Bioinformatics Analysis of Outer Capsid Protein VP7 gene for Giant Panda Rotavirus CH-1 Strain
Author: YAN Qi-gui, LEI Yan, ZHANG Zhi-he, WANG Cheng-dong, YANG Ai-guo, WANG Xu, ZUO Lan, XIAO Yang
Journal: Chinese Journal of Animal and Veterinary Sciences
Year: 2010
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18)Title: Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism
Author: Pietro D. Spanu, James C. Abbott, Joelle Amselem, Timothy A. Burgis, Darren M. Soanes, Kurt Stüber, Emiel Ver Loren van Themaat, James K. M. Brown, Sarah A. Butcher, Sarah J. Gurr, Marc-Henri Lebrun, Christopher J. Ridout, Paul Schulze-Lefert, Nicholas J. Talbot, Nahal Ahmadinejad, Christian Ametz, Geraint R. Barton, Mariam Benjdia, Przemyslaw Bidzinski, Laurence V. Bindschedler, Maike Both, Marin T. Brewer, Lance Cadle-Davidson, Molly M. Cadle-Davidson, Jerome Collemare, Rainer Cramer, Omer Frenkel, Dale Godfrey, James Harriman, Claire Hoede, Brian C. King, Sven Klages, Jochen Kleemann, Daniela Knoll, Prasanna S. Koti, Jonathan Kreplak, Francisco J. López-Ruiz, Xunli Lu, Takaki Maekawa, Siraprapa Mahanil, Cristina Micali, Michael G. Milgroom, Giovanni Montana, Sandra Noir, Richard J. O’Connell, Simone Oberhaensli, Francis Parlange, Carsten Pedersen, Hadi Quesneville, Richard Reinhardt, Matthias Rott, Soledad Sacristán, Sarah M. Schmidt, Moritz Schön, Pari Skamnioti, Hans Sommer, Amber Stephens, Hiroyuki Takahara, Hans Thordal-Christensen, Marielle Vigouroux, Ralf Weßling, Thomas Wicker, Ralph Panstruga
Journal: Science
Year: 2010
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19)Title: Genome mining of mycosporine-like amino acid (MAA) synthesizing and non-synthesizing cyanobacteria: A bioinformatics study
Author: Shailendra P. Singh, Manfred Klisch, Rajeshwar P. Sinha, Donat-P. Häder
Journal: Genomics
Year: 2010
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20)Title: Identifying and Quantifying Orphan Protein Sequences in Fungi
Author: Diana Ekman, Arne Elofsson
Journal: Journal of Molecular Biology
Year: 2010
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21)Title: Inference of Homologous Recombination in Bacteria Using Whole-Genome Sequences
Author: Xavier Didelot, Daniel Lawson, Aaron Darling and Daniel Falush
Journal: Genetics December
Year: 2010
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22)Title: Insights into the structure, function and evolution of the radical-SAM 23S rRNA methyltransferase Cfr that confers antibiotic resistance in bacteria
Author: Katarzyna H. Kaminska, Elzbieta Purta, Lykke H. Hansen, Janusz M. Bujnicki, Birte Vester and Katherine S. Long
Journal: Nucleic Acids Research
Year: 2010
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23)Title: Intra-isolate genome variation in arbuscular mycorrhizal fungi persists in the transcriptome
Author: E. BOON, E. ZIMMERMAN, B. F. LANG, M. HIJRI
Journal: Journal of Evolutionary Biology
Year: 2010
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24)Title: ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases
Author: Eva Bellemain, Tor Carlsen, Christian Brochmann, Eric Coissac, Pierre Taberlet and Håvard Kauserud
Journal: BMC Bioinformatics
Year: 2010
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25)Title: Lessons from the genomes of extremely acidophilic bacteria and archaea with special emphasis on bioleaching microorganisms
Author: Juan Pablo Cárdenas, Jorge Valdés, Raquel Quatrini, Francisco Duarte, David S. Holmes
Journal: Applied Microbiology and Biotechnology
Year: 2010
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26)Title: MIRU-VNTRplus: a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria
Author: Thomas Weniger, Justina Krawczyk, Philip Supply, Stefan Niemann and Dag Harmsen
Journal: Nucleic Acids Research
Year: 2010
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27)Title: Molecular diversity of arbuscular mycorrhizal fungi and their distribution patterns related to host-plants and habitats in a hot and arid ecosystem, southwest China
Author: Ling-Fei Li, Tao Li, Yan Zhang, Zhi-Wei Zhao
Journal: FEMS Microbiology Ecology
Year: 2010
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28)Title: Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi
Author: Jason C. Slot and Antonis Rokas
Journal: Proceedings of the National Academy of Sciences
Year: 2010
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29)Title: Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea
Author: Walker CB, de la Torre JR, Klotz MG, Urakawa H, Pinel N, Arp DJ, Brochier-Armanet C, Chain PS, Chan PP, Gollabgir A, Hemp J, Hügler M, Karr EA, Könneke M, Shin M, Lawton TJ, Lowe T, Martens-Habbena W, Sayavedra-Soto LA, Lang D, Sievert SM, Rosenzweig AC, Manning G, Stahl DA
Journal: Proc Natl Acad Sci U S A
Year: 2010
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30)Title: Novel approaches for analysing gut microbes and dietary polyphenols: challenges and opportunities
Author: R. A. Kemperman, S. Bolca, L. C. Roger and E. E. Vaughan
Journal: Microbiology
Year: 2010
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31)Title: Palaeophylogenomics of the Vertebrate Ancestor—Impact of Hidden Paralogy on Hagfish and Lamprey Gene Phylogeny
Author: Shigehiro Kuraku
Journal: Integr. Comp. Biol.
Year: 2010
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32)Title: Pectolytic bacteria associated with soft rot of dieffenbachia (Dieffenbachia maculata)
Author: Mikicin´ski, A.; Pulawska, J.; Sobiczewski, P.; Orlikowski, L. B.
Journal: Phytopathologia
Year: 2010
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33)Title: Phylogenetic species delimitation in ectomycorrhizal fungi and implications for barcoding: the case of the Tricholoma scalpturatum complex (Basidiomycota)
Author: PATRICIA JARGEAT, FLORENT MARTOS, FABIAN CARRICONDE, HERVÉ GRYTA, PIERRE-ARTHUR MOREAU, MONIQUE GARDES
Journal:  Molecular Ecology
Year: 2010
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34)Title: Proteomics, Genomics, and Pathway Analyses of Escherichia coli and Staphylococcus aureus Infected Milk Whey Reveal Molecular Pathways and Networks Involved in Mastitis
Author: Eveline M. Ibeagha-Awemu, Aloysius E. Ibeagha, Serge Messier and Xin Zhao
Journal: J. Proteome Res.
Year: 2010
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35)Title: Recent progress and new challenges in metagenomics for biotechnology
Author: Ludmila Chistoserdova
Journal: Biotechnology Letters
Year: 2010
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36)Title: Structure, function, and evolution of the Thiomonas spp. genome
Author: Arsène-Ploetze F, Koechler S, Marchal M, Coppée JY, Chandler M, Bonnefoy V, Brochier-Armanet C, Barakat M, Barbe V, Battaglia-Brunet F, Bruneel O, Bryan CG, Cleiss-Arnold J, Cruveiller S, Erhardt M, Heinrich-Salmeron A, Hommais F, Joulian C, Krin E, Lieutaud A, Lièvremont D, Michel C, Muller D, Ortet P, Proux C, Siguier P, Roche D, Rouy Z, Salvignol G, Slyemi D, Talla E, Weiss S, Weissenbach J, Médigue C, Bertin PN.
Journal: PLoS Genet.
Year: 2010
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37)Title: The ecological coherence of high bacterial taxonomic ranks
Author: Laurent Philippot, Siv G. E. Andersson, Tom J. Battin, James I. Prosser, Joshua P. Schimel, William B. Whitman and Sara Hallin
Journal: Nature Reviews Microbiology
Year: 2010
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38)Title: The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves
Author: Amanda J. Redford, Robert M. Bowers, Rob Knight, Yan Linhart, Noah Fierer
Journal: Environmental Microbiology
Year: 2010
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39)Title: The obligate endobacteria of arbuscular mycorrhizal fungi are ancient heritable components related to the Mollicutes
Author: Maria Naumann, Arthur SchuBler and Paola Bonfante
Journal: The ISME Journal
Year: 2010
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40)Title: The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota)
Author: M. Öpik, A. Vanatoa, E. Vanatoa, M. Moora, J. Davison, J. M. Kalwij, Ü. Reier, M. Zobel
Journal: New Phytologist
Year: 2010
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41)Title: When metagenomics meets stable-isotope probing: progress and perspectives
Author: Yin Chen, J. Colin Murrell
Journal: Trends in Microbiology
Year: 2010
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42)Title: Whole-genome based Archaea phylogeny and taxonomy: A composition vector approach
Author: SUN JianDong, XU Zhao & HAO BaiLin
Journal: Chinese Science Bulletin
Year: 2010
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43)Title: Zinc proteomes, phylogenetics and evolution
Author: Leonardo Decaria , Ivano Bertini and Robert J. P. Williams
Journal: Metallomics
Year: 2010
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