Academic literature on the topic 'Bioinformatics; Bioremediation'

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Journal articles on the topic "Bioinformatics; Bioremediation"

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Pazos, F. "MetaRouter: bioinformatics for bioremediation." Nucleic Acids Research 33, Database issue (2004): D588—D592. http://dx.doi.org/10.1093/nar/gki068.

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Kumar, S. Senthil, S. Shantkriti, T. Muruganandham, E. Murugesh, Niraj Rane, and S. P. Govindwar. "Bioinformatics aided microbial approach for bioremediation of wastewater containing textile dyes." Ecological Informatics 31 (January 2016): 112–21. http://dx.doi.org/10.1016/j.ecoinf.2015.12.001.

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Trifi, Houda, Afef Najjari, Wafa Achouak, et al. "Metataxonomics of Tunisian phosphogypsum based on five bioinformatics pipelines: Insights for bioremediation." Genomics 112, no. 1 (2020): 981–89. http://dx.doi.org/10.1016/j.ygeno.2019.06.014.

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Biggs, Matthew B., and Jason A. Papin. "Metabolic network-guided binning of metagenomic sequence fragments." Bioinformatics 32, no. 6 (2015): 867–74. http://dx.doi.org/10.1093/bioinformatics/btv671.

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Abstract Motivation: Most microbes on Earth have never been grown in a laboratory, and can only be studied through DNA sequences. Environmental DNA sequence samples are complex mixtures of fragments from many different species, often unknown. There is a pressing need for methods that can reliably reconstruct genomes from complex metagenomic samples in order to address questions in ecology, bioremediation, and human health. Results: We present the SOrting by NEtwork Completion (SONEC) approach for assigning reactions to incomplete metabolic networks based on a metabolite connectivity score. We successfully demonstrate proof of concept in a set of 100 genome-scale metabolic network reconstructions, and delineate the variables that impact reaction assignment accuracy. We further demonstrate the integration of SONEC with existing approaches (such as cross-sample scaffold abundance profile clustering) on a set of 94 metagenomic samples from the Human Microbiome Project. We show that not only does SONEC aid in reconstructing species-level genomes, but it also improves functional predictions made with the resulting metabolic networks. Availability and implementation: The datasets and code presented in this work are available at: https://bitbucket.org/mattbiggs/sorting_by_network_completion/. Contact: papin@virginia.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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Miralles-Robledillo, Jose María, Javier Torregrosa-Crespo, Rosa María Martínez-Espinosa, and Carmen Pire. "DMSO Reductase Family: Phylogenetics and Applications of Extremophiles." International Journal of Molecular Sciences 20, no. 13 (2019): 3349. http://dx.doi.org/10.3390/ijms20133349.

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Dimethyl sulfoxide reductases (DMSO) are molybdoenzymes widespread in all domains of life. They catalyse not only redox reactions, but also hydroxylation/hydration and oxygen transfer processes. Although literature on DMSO is abundant, the biological significance of these enzymes in anaerobic respiration and the molecular mechanisms beyond the expression of genes coding for them are still scarce. In this review, a deep revision of the literature reported on DMSO as well as the use of bioinformatics tools and free software has been developed in order to highlight the relevance of DMSO reductases on anaerobic processes connected to different biogeochemical cycles. Special emphasis has been addressed to DMSO from extremophilic organisms and their role in nitrogen cycle. Besides, an updated overview of phylogeny of DMSOs as well as potential applications of some DMSO reductases on bioremediation approaches are also described.
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Miller, Ryan K., Robert M. Kirkham, and Adam J. Kleinschmit. "Bioinformatics Analysis of Microbial Abundance and Diversity in Acid Mine Drainage from the Solomon Mine Near Creede, Colorado." Fine Focus 4, no. 1 (2018): 41–65. http://dx.doi.org/10.33043/ff.4.1.41-65.

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This study focused on characterizing the phylotypic composition of acid mine drainage (AMD) communities associated with the Solomon Mine near Creede, Colorado, and its relative diversity compared to microbial communities found in the East Willow Creek (EWC) watershed. AMD from the Solomon Mine adit flows into an existing passive bioremediation wetland system located next to the Solomon Mine adit that currently is ineffective and is under consideration for renovation. We are interested in gaining an understanding of the baseline microbial communities present in AMD/EWC and to monitor them during future wetland renovation. Prokaryotic community profiling was approached using SSU 16S rRNA marker gene amplification coupled with next generation sequencing. Bioinformatics analysis included raw read preprocessing, data visualization, and statistical testing using a combination of USEARCH and QIIME-based scripts. A pH and conductivity gradient were observed for water moving through the currently inefficient wetland system at the Solomon Mine. The EWC microbiomes had statistically significant higher alpha diversity compared to the AMD microbiomes. Beta diversity analysis parsed the sample locations into statistically significant groups including core AMD microbiomes, the wetland Cell 3 microbiome, and EWC microbiomes using multidimensional scaling. Taxa driving beta diversity included the phylum Proteobacteria for the core AMD microbiomes, the phyla Firmicutes and Chloroflexi for the constructed wetland Cell 3, and the phyla Bacteroidetes and Verrucomicrobia for EWC. Our data suggests that the microbial community in constructed wetland Cell 3 is likely where limited sulfate reduction activity is operating at low capacity, which will be further investigated via shotgun metagenomic analysis.
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Setlhare, Boitumelo, Ajit Kumar, Mduduzi Mokoena, and Ademola Olaniran. "Catechol 1,2-Dioxygenase is an Analogue of Homogentisate 1,2-Dioxygenase in Pseudomonas chlororaphis Strain UFB2." International Journal of Molecular Sciences 20, no. 1 (2018): 61. http://dx.doi.org/10.3390/ijms20010061.

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Catechol dioxygenases in microorganisms cleave catechol into cis-cis-muconic acid or 2-hydroxymuconic semialdehyde via the ortho- or meta-pathways, respectively. The aim of this study was to purify, characterize, and predict the template-based three-dimensional structure of catechol 1,2-dioxygenase (C12O) from indigenous Pseudomonas chlororaphis strain UFB2 (PcUFB2). Preliminary studies showed that PcUFB2 could degrade 40 ppm of 2,4-dichlorophenol (2,4-DCP). The crude cell extract showed 10.34 U/mL of C12O activity with a specific activity of 2.23 U/mg of protein. A 35 kDa protein was purified to 1.5-fold with total yield of 13.02% by applying anion exchange and gel filtration chromatography. The enzyme was optimally active at pH 7.5 and a temperature of 30 °C. The Lineweaver–Burk plot showed the vmax and Km values of 16.67 µM/min and 35.76 µM, respectively. ES-MS spectra of tryptic digested SDS-PAGE band and bioinformatics studies revealed that C12O shared 81% homology with homogentisate 1,2-dioxygenase reported in other Pseudomonas chlororaphis strains. The characterization and optimization of C12O activity can assist in understanding the 2,4-DCP metabolic pathway in PcUFB2 and its possible application in bioremediation strategies.
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Peng, Tao, An Luo, Jie Kan, Lei Liang, Tongwang Huang, and Zhong Hu. "Identification of A Ring-Hydroxylating Dioxygenases Capable of Anthracene and Benz[a]anthracene Oxidization from Rhodococcus sp. P14." Journal of Molecular Microbiology and Biotechnology 28, no. 4 (2018): 183–89. http://dx.doi.org/10.1159/000494384.

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Nowadays, contamination of soil and marine sediments by polycyclic aromatic hydrocarbons (PAHs) has become a serious problem all over the world. <i>Rhodococcus</i> sp. P14 was isolated from sediments with crude oil contaminate and showed degradation ability on various PAHs. The genome of <i>Rhodococcus</i> sp. P14 was sequenced. A gene cluster encoding a ring-hydroxylating dioxygenase Baa related to PAH degradation was identified by bioinformatics. The expression level of gene <i>baaA</i> was increased when P14 was cultured with anthracene, pyrene, phenanthrene, or benz[a]­anthracene as the single carbon source. The recombinant protein Baa was overexpressed in <i>E. coli</i> BL21 (DE3). Further investigations on the recombinant protein Baa in <i>E. coli</i> demonstrated that it was able to oxidize anthracene and benz [a]anthracene, resulting in 9,10-dihydroxyanthracene and 7, 12-dihydroxybenz[a]anthracene as metabolites, respectively. These results indicate that Baa plays an important role in PAH degradation in <i>Rhodococcus</i> sp. P14 and Baa has potential application in the bioremediation of PAHs in the contaminated environment.
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Li, Jiangwei, Anyi Hu, Shijie Bai, et al. "Characterization and Performance of Lactate-Feeding Consortia for Reductive Dechlorination of Trichloroethene." Microorganisms 9, no. 4 (2021): 751. http://dx.doi.org/10.3390/microorganisms9040751.

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Understanding the underlying mechanism that drives the microbial community mediated by substrates is crucial to enhance the biostimulation in trichloroethene (TCE)-contaminated sites. Here, we investigated the performance of stable TCE-dechlorinating consortia by monitoring the variations in TCE-related metabolites and explored their underlying assembly mechanisms using 16S rDNA amplicon sequencing and bioinformatics analyses. The monitoring results indicated that three stable TCE-dechlorinating consortia were successfully enriched by lactate-containing anaerobic media. The statistical analysis results demonstrated that the microbial communities of the enrichment cultures changed along with time and were distinguished by their sample sources. The deterministic and stochastic processes were simultaneously responsible for shaping the TCE-dechlorinating community assembly. The indicator patterns shifted with the exhaustion of the carbon source and the pollutants, and the tceA-carrying Dehalococcoides, as an indicator for the final stage samples, responded positively to TCE removal during the incubation period. Pseudomonas, Desulforhabdus, Desulfovibrio and Methanofollis were identified as keystone populations in the TCE-dechlorinating process by co-occurrence network analysis. The results of this study indicate that lactate can be an effective substrate for stimulated bioremediation of TCE-contaminated sites, and the reduction of the stochastic forces or enhancement of the deterministic interventions may promote more effective biostimulation.
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Bernabeu, Eric, Jose María Miralles-Robledillo, Micaela Giani, Elena Valdés, Rosa María Martínez-Espinosa, and Carmen Pire. "In Silico Analysis of the Enzymes Involved in Haloarchaeal Denitrification." Biomolecules 11, no. 7 (2021): 1043. http://dx.doi.org/10.3390/biom11071043.

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During the last century, anthropogenic activities such as fertilization have led to an increase in pollution in many ecosystems by nitrogen compounds. Consequently, researchers aim to reduce nitrogen pollutants following different strategies. Some haloarchaea, owing to their denitrifier metabolism, have been proposed as good model organisms for the removal of not only nitrate, nitrite, and ammonium, but also (per)chlorates and bromate in brines and saline wastewater. Bacterial denitrification has been extensively described at the physiological, biochemical, and genetic levels. However, their haloarchaea counterparts remain poorly described. In previous work the model structure of nitric oxide reductase was analysed. In this study, a bioinformatic analysis of the sequences and the structural models of the nitrate, nitrite and nitrous oxide reductases has been described for the first time in the haloarchaeon model Haloferax mediterranei. The main residues involved in the catalytic mechanism and in the coordination of the metal centres have been explored to shed light on their structural characterization and classification. These results set the basis for understanding the molecular mechanism for haloarchaeal denitrification, necessary for the use and optimization of these microorganisms in bioremediation of saline environments among other potential applications including bioremediation of industrial waters.
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Dissertations / Theses on the topic "Bioinformatics; Bioremediation"

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Elekwachi, Chijioke Obioma. "Bioinformatics resources to support bioremediation research." Thesis, University of Nottingham, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.595818.

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Contamination of ecosystems by xenobiotic substances has led to significant negative impacts on the ecologies and on the health and economic livelihood of the human populations in affected environments. Bioremediation, particularly microbial bioremediation, has proven to be a safe, low-cost and environmentally friendly method for remediation of such areas. However, a lack of complete understanding of the metabolic, enzymatic and cellular processes involved has made it difficult to model and predict outcomes of field processes. The ability of researchers to make critical decisions capable of influencing the direction and outcomes of these processes is also hampered. This study outlines the results of a survey and describes the electronic Microbial BioRemediation (eMBR) web portal, designed to improve collaboration in the bioremediation research community. It describes the structure, algorithms and output of three bioinformatics resources developed and deployed via the portal. eMBRLitMine addresses the problem of identifying which microorganisms would be suitable for remediating sites contaminated by named compounds. It combines named-entity recognition algorithms, a mySQL database, graph rendering technologies and Perl scripts to create, from the vast information available within published literature, a statistical co-occurrence matrix which it uses to infer possible associations between microorganisms and particular contaminants. This provides valuable insights into possible bacteria/contaminant relationships and highlights bacterial species that could be used in remediation of specified contaminants. eMBRCatalogue is a moderated and searchable database cataloguing bioremediation case studies. Implemented as an eXtensible Markup Language (XML) database employing a user-generated-content framework, it provides background knowledge necessary for planning and execution of bioremediation activities. Developed following the construction of a comprehensive metabolic biodegradation network, eMBRHelper enables the delineation of possible biodegradation pathways for named contaminants. By integrating relevant chemical, enzymatic and genomics information, it attempts to model the interplay between contaminants, enzymes, microorganisms and degradation pathway, enabling researchers to make informed decisions for improved outcomes, particularly for remediation exercises involving bioaugmentation. The study also analysed usage of the portal and resources, made recommendations for future developments and highlights avenues for further informatics support for the bioremediation research sector.
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Greated, Alicia. "The IncP-9 plasmid group : characterisation of genomic sequences and development of tools for environmental monitoring." Thesis, University of Birmingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.366379.

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Keter, Nancy Rop. "Site-Directed Mutagenesis of Glutathione Transferase, GstB from Escherichia coli for Use in Bioremediation." Youngstown State University / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=ysu1620836630780629.

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Jones, Katy June. "Bioinformatic analysis of biotechnologically important microbial communities." Thesis, University of Exeter, 2018. http://hdl.handle.net/10871/34543.

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Difficulties associated with the study of microbial communities, such as low proportions of cultivable species, have been addressed in recent years with the advent of a range of sequencing technologies and bioinformatic tools. This is enabling previously unexplored communities to be characterised and utilised in a range of biotechnology applications. In this thesis bioinformatic methods were applied to two datasets of biotechnological interest: microbial communities found living with the oil-producing alga Botryococcus braunii and microbial communities in acid mine drainage (AMD). B. braunii is of high interest to the biofuel industry due to its ability to produce high amounts of oils, in the form of hydrocarbons. However, a number of factors, including low growth rates, have prevented its cultivation on an industrial scale. Studies show B. braunii lives in a consortium with numerous bacteria which may influence its growth. This thesis reports both whole genome analysis and 16S rRNA gene sequence analysis to gain a greater understanding of the B. braunii bacterial consortium. Bacteria have been identified, some of which had not previously been documented as living with B. braunii, and evidence is presented for ways in which they may influence growth of the alga, including B-vitamin synthesis and secretion systems. AMD is a worldwide problem, polluting the environment and negatively impacting on human health. This by-product of the mining industry is a problem in the South West of England, where disused metalliferous mines are now a source of AMD. Bioremediation of AMD is an active area of research; sulphur-reducing bacteria and other bacteria which can remove toxic metals from AMD can be utilised for this purpose. Identifying bacteria and archaea that are able to thrive in AMD and which also have these bioremediation properties is therefore of great importance. Metagenomic sequencing has been carried out on the microbial community living in AMD sediment at the Wheal Maid tailings lagoon near Penryn in Cornwall. From these data have been identified a diverse range of bacteria and archaea present at both the sediment surface level and at depth, including microorganisms closely related to taxa reported from metalliferous mines on other continents. Evidence has been found of sulphur-reducing bacteria and of pathways for various other bioremediation-linked processes.
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Books on the topic "Bioinformatics; Bioremediation"

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Biotechnology and bioinformatics: Advances and applications for bioenergy, bioremediation, and biopharmaceutical research. Apple Academic Press, 2015.

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Book chapters on the topic "Bioinformatics; Bioremediation"

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Fulekar, M. H. "Environmental Cleanup Approach Using Bioinformatics in Bioremediation." In Bioinformatics: Applications in Life and Environmental Sciences. Springer Netherlands, 2009. http://dx.doi.org/10.1007/978-1-4020-8880-3_10.

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Slama, Houda Ben, Hafsa Cherif-Silini, Ali Chenari Bouket, et al. "Biotechnology and Bioinformatics of Endophytes in Biocontrol, Bioremediation, and Plant Growth Promotion." In Endophytes: Mineral Nutrient Management, Volume 3. Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-65447-4_8.

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Thatoi, H. N., and S. K. Pradhan. "Detoxification and Bioremediation of Hexavalent Chromium Using Microbes and Their Genes: An Insight into Genomic, Proteomic and Bioinformatics Studies." In Microbial Biotechnology. Springer Singapore, 2017. http://dx.doi.org/10.1007/978-981-10-6847-8_13.

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Singh, Desh Deepak. "Bioinformatics and Applications in Biotechnology." In Microbes for Sustainable Development and Bioremediation. CRC Press, 2019. http://dx.doi.org/10.1201/9780429275876-20.

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Kumari, Priyanka, and Yogesh Kumar. "Bioinformatics and computational tools in bioremediation and biodegradation of environmental pollutants." In Bioremediation for Environmental Sustainability. Elsevier, 2021. http://dx.doi.org/10.1016/b978-0-12-820318-7.00019-8.

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Bhatt, Pankaj. "Insilico Tools to Study the Bioremediation in Microorganisms." In Handbook of Research on Microbial Tools for Environmental Waste Management. IGI Global, 2018. http://dx.doi.org/10.4018/978-1-5225-3540-9.ch018.

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Bioinformatics is the new area of science to study various living organisms, plants and animals. Bioremediation is the removal of toxic pollutants from the environment using microorganisms. Many of the databases are available online and can be used for the study of the microorganism genomics, transcriptomics, proteomics. This chapter mainly focuses the uses of recent databases and tools for the exploration of microorganisms.
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Singh, Jyoti, Madhuri Gupta, Kaushalendra Kumar Singh, et al. "Advancement in bioinformatics and microarray-based technologies for genome sequence analysis and its application in bioremediation of soil and water pollutants." In Microbe Mediated Remediation of Environmental Contaminants. Elsevier, 2021. http://dx.doi.org/10.1016/b978-0-12-821199-1.00018-3.

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Conference papers on the topic "Bioinformatics; Bioremediation"

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Ladygina, Valentina P., Irina V. Trusey, and Yury L. Gurevich. "Bioremediation of the Fuel Oil Contaminated Subsurface." In 2008 2nd International Conference on Bioinformatics and Biomedical Engineering. IEEE, 2008. http://dx.doi.org/10.1109/icbbe.2008.549.

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Zou, Yi, Haibo Li, Yi Zou, and Haibo Li. "Microorganisms in Rivers in the Application of Bioremediation." In 2010 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE). IEEE, 2010. http://dx.doi.org/10.1109/icbbe.2010.5515582.

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Liu, Xia, Xihong Li, Baoli Cai, and Songwen Wang. "Bioremediation of Atrazine Contaminated Soil by Arthrobacter SP. Strain AD4." In 2010 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE). IEEE, 2010. http://dx.doi.org/10.1109/icbbe.2010.5515952.

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Li, Chuan, Yun Bai, and Zhaojie Jiao. "Influence of Pollution Concentration on Bioremediation of Petroleum-Contaminated Soil." In 2010 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE). IEEE, 2010. http://dx.doi.org/10.1109/icbbe.2010.5516310.

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Song, Xinyuan, and Jianbing Li. "Application of Hog Fuel for the Bioremediation of Oil Contaminated Soils." In 2010 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE). IEEE, 2010. http://dx.doi.org/10.1109/icbbe.2010.5517455.

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Li, Yu-Ying. "The Influences of Tween60 and Rhamnolipid on the Bioremediation of n-Hexadecane." In 2010 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE). IEEE, 2010. http://dx.doi.org/10.1109/icbbe.2010.5517582.

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Wang, Yang, and Qiuyu Wang. "Notice of Retraction: A New Member for Bioremediation of Crude Oil Contaminated Soil." In 2011 5th International Conference on Bioinformatics and Biomedical Engineering. IEEE, 2011. http://dx.doi.org/10.1109/icbbe.2011.5781354.

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Jia, Jianli, Juan Peng, Ying Liu, et al. "Micro-Ecosystem and Its Influence to the Bioremediation Feasibility of Oil Contaminated Soils." In 2010 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE). IEEE, 2010. http://dx.doi.org/10.1109/icbbe.2010.5516299.

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Lang, Yanhong, Xingchun Li, and Yaping Fu. "Enhanced Bioremediation of Heavy Oil Contaminated Soil by Bacterial Consortium Amended with Biosurfactant." In 2010 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE). IEEE, 2010. http://dx.doi.org/10.1109/icbbe.2010.5517206.

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Ma, Yuexuan, Zhao Jiang, Yao Ma, Juan Du, and Ying Zhang. "Combined Bioremediation of Atrazine Contaminated Soil by Two Atrazine Degrading Strains and Grass." In 2010 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE). IEEE, 2010. http://dx.doi.org/10.1109/icbbe.2010.5517374.

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