Relevant bibliographies by topics / Genomic DNA of E.coli analysis

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
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Academic literature on the topic 'Genomic DNA of E.coli analysis'

Author: Grafiati
Published: 4 June 2021
Last updated: 7 February 2022

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Journal articles on the topic "Genomic DNA of E.coli analysis"

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Vilen, Heikki, Juha-Matti Aalto, Anna Kassinen, Lars Paulin, and Harri Savilahti. "A Direct Transposon Insertion Tool for Modification and Functional Analysis of Viral Genomes." Journal of Virology 77, no. 1 (2003): 123–34. http://dx.doi.org/10.1128/jvi.77.1.123-134.2003.

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ABSTRACT Advances in DNA transposition technology have recently generated efficient tools for various types of functional genetic analyses. We demonstrate here the power of the bacteriophage Mu-derived in vitro DNA transposition system for modification and functional characterization of a complete bacterial virus genome. The linear double-stranded DNA genome of Escherichia coli bacteriophage PRD1 was studied by insertion mutagenesis with reporter mini-Mu transposons that were integrated in vitro into isolated genomic DNA. After introduction into bacterial cells by electroporation, recombinant
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Dobrindt, Ulrich, Franziska Agerer, Kai Michaelis, et al. "Analysis of Genome Plasticity in Pathogenic and Commensal Escherichia coli Isolates by Use of DNA Arrays." Journal of Bacteriology 185, no. 6 (2003): 1831–40. http://dx.doi.org/10.1128/jb.185.6.1831-1840.2003.

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ABSTRACT Genomes of prokaryotes differ significantly in size and DNA composition. Escherichia coli is considered a model organism to analyze the processes involved in bacterial genome evolution, as the species comprises numerous pathogenic and commensal variants. Pathogenic and nonpathogenic E. coli strains differ in the presence and absence of additional DNA elements contributing to specific virulence traits and also in the presence and absence of additional genetic information. To analyze the genetic diversity of pathogenic and commensal E. coli isolates, a whole-genome approach was applied.
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Kang, Yujin, Jinyong Lee, Jisoo Kim, et al. "Analysis of alcohol-induced DNA damage in Escherichia coli by visualizing single genomic DNA molecules." Analyst 141, no. 14 (2016): 4326–31. http://dx.doi.org/10.1039/c6an00616g.

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Baumler, David J., Lois M. Banta, Kai F. Hung, et al. "Using Comparative Genomics for Inquiry-Based Learning to Dissect Virulence of Escherichia coli O157:H7 and Yersinia pestis." CBE—Life Sciences Education 11, no. 1 (2012): 81–93. http://dx.doi.org/10.1187/cbe.10-04-0057.

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Genomics and bioinformatics are topics of increasing interest in undergraduate biological science curricula. Many existing exercises focus on gene annotation and analysis of a single genome. In this paper, we present two educational modules designed to enable students to learn and apply fundamental concepts in comparative genomics using examples related to bacterial pathogenesis. Students first examine alignments of genomes of Escherichia coli O157:H7 strains isolated from three food-poisoning outbreaks using the multiple-genome alignment tool Mauve. Students investigate conservation of virule
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CAO, YINHE, WEN-WEN TUNG, J. B. GAO, and YAN QI. "RECURRENCE TIME STATISTICS: VERSATILE TOOLS FOR GENOMIC DNA SEQUENCE ANALYSIS." Journal of Bioinformatics and Computational Biology 03, no. 03 (2005): 677–96. http://dx.doi.org/10.1142/s0219720005001235.

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With the completion of the human and a few model organisms' genomes, and with the genomes of many other organisms waiting to be sequenced, it has become increasingly important to develop faster computational tools which are capable of easily identifying the structures and extracting features from DNA sequences. One of the more important structures in a DNA sequence is repeat-related. Often they have to be masked before protein coding regions along a DNA sequence are to be identified or redundant expressed sequence tags (ESTs) are to be sequenced. Here we report a novel recurrence time-based me
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Herbelin, Corinne J., Samantha C. Chirillo, Kristen A. Melnick, and Thomas S. Whittam. "Gene Conservation and Loss in themutS-rpoS Genomic Region of PathogenicEscherichia coli." Journal of Bacteriology 182, no. 19 (2000): 5381–90. http://dx.doi.org/10.1128/jb.182.19.5381-5390.2000.

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ABSTRACT The extent and nature of DNA polymorphism in themutS-rpoS region of the Escherichia coli genome were assessed in 21 strains of enteropathogenic E. coli(EPEC) and enterohemorrhagic E. coli (EHEC) and in 6 strains originally isolated from natural populations. The intervening region between mutS and rpoS was amplified by long-range PCR, and the resulting amplicons varied substantially in length (7.8 to 14.2 kb) among pathogenic groups. Restriction maps based on five enzymes and sequence analysis showed that strains of the EPEC 1, EPEC 2, and EHEC 2 groups have a long mutS-rpoS region com
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Grozdanov, Lubomir, Carsten Raasch, Jürgen Schulze, et al. "Analysis of the Genome Structure of the Nonpathogenic Probiotic Escherichia coli Strain Nissle 1917." Journal of Bacteriology 186, no. 16 (2004): 5432–41. http://dx.doi.org/10.1128/jb.186.16.5432-5441.2004.

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ABSTRACT Nonpathogenic Escherichia coli strain Nissle 1917 (O6:K5:H1) is used as a probiotic agent in medicine, mainly for the treatment of various gastroenterological diseases. To gain insight on the genetic level into its properties of colonization and commensalism, this strain's genome structure has been analyzed by three approaches: (i) sequence context screening of tRNA genes as a potential indication of chromosomal integration of horizontally acquired DNA, (ii) sequence analysis of 280 kb of genomic islands (GEIs) coding for important fitness factors, and (iii) comparison of Nissle 1917
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Parekh, Virali J., Frank Wien, Wilfried Grange, Thomas A. De Long, Véronique Arluison, and Richard R. Sinden. "Crucial Role of the C-Terminal Domain of Hfq Protein in Genomic Instability." Microorganisms 8, no. 10 (2020): 1598. http://dx.doi.org/10.3390/microorganisms8101598.

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G-rich DNA repeats that can form G-quadruplex structures are prevalent in bacterial genomes and are frequently associated with regulatory regions of genes involved in virulence, antigenic variation, and antibiotic resistance. These sequences are also inherently mutagenic and can lead to changes affecting cell survival and adaptation. Transcription of the G-quadruplex-forming repeat (G3T)n in E. coli, when mRNA comprised the G-rich strand, promotes G-quadruplex formation in DNA and increases rates of deletion of G-quadruplex-forming sequences. The genomic instability of G-quadruplex repeats may
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Willenbrock, Hanni, Anne Petersen, Camilla Sekse, Kristoffer Kiil, Yngvild Wasteson, and David W. Ussery. "Design of a Seven-Genome Escherichia coli Microarray for Comparative Genomic Profiling." Journal of Bacteriology 188, no. 22 (2006): 7713–21. http://dx.doi.org/10.1128/jb.01043-06.

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ABSTRACT We describe the design and evaluate the use of a high-density oligonucleotide microarray covering seven sequenced Escherichia coli genomes in addition to several sequenced E. coli plasmids, bacteriophages, pathogenicity islands, and virulence genes. Its utility is demonstrated for comparative genomic profiling of two unsequenced strains, O175:H16 D1 and O157:H7 3538 (Δstx 2::cat) as well as two well-known control strains, K-12 W3110 and O157:H7 EDL933. By using fluorescently labeled genomic DNA to query the microarrays and subsequently analyze common virulence genes and phage elements
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Gomez-Duarte, Oscar, Julio Guerra, and Ricky Ko. "1127. Genomic Analysis of Biofilm-Forming Enteroinvasive E. coli Emergent Pathogen." Open Forum Infectious Diseases 5, suppl_1 (2018): S337—S338. http://dx.doi.org/10.1093/ofid/ofy210.960.

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Abstract Background Enteroinvasive Escherichia coli (EIEC) are involved in dysenteric diarrhea among children in low- and middle-income countries. EIEC strains isolated in Colombia, South America were shown to form biofilms and to be invasive in vitro. The O96:H19 serotypes and biofilm formation (BF) are not common phenotypes among EIEC, and the role they may play in diarrhea is at present unknown. The main goal of this study was to identify virulence and BF genes from EIEC genomic data. We hypothesize that EIEC O96:H19 strain 52.1 originated from horizontal transfer of a Shigella-like virulen
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Dissertations / Theses on the topic "Genomic DNA of E.coli analysis"

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Walters, D. E. "A further nar gene in Escherichia coli." Thesis, University of Leeds, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.383761.

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Cockram, Charlotte Anne. "Genomic analysis of RecA-DNA interactions during double-strand break repair in Escherichia coli." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/17284.

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Maintaining genomic integrity is crucial for cell survival. In Escherichia coli, Rec-Amediated homologous recombination (HR) plays an essential role in the repair of DNA double-strand breaks (DSB) and the SOS response through a series of highly dynamic interactions with the chromosome. A greater understanding of the mechanism of homologous recombination requires quantitative analysis of genomic studies in live cells. The aim of this thesis was to investigate the dynamics of the RecA-DNA interactions in vivo following the induction of a site-specific DSB in the chromosome of E. coli. This DSB i
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Lundmark, Per Erik. "Genetic and Genomic Analysis of DNA Sequence Variation." Doctoral thesis, Uppsala universitet, Molekylär medicin, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-158486.

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The studies in this thesis describe the application of genotyping and allele specific expression analysis to genetic studies. The role of the gene NPC1 in Triglyceride metabolism was explored in mouse models and in humans on the population level in study I. NPC1 was found to affect hepatic triglyceride metabolism, and to be relevant for controlling serum triglyceride levels in mice and potentially in humans. In study II the utility of the HapMap CEU samples was investigated for tagSNP selection in six European populations. The HapMap CEU was found to be representative for tagSNP selection in a
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Eresh, Salih. "Karyotype analysis and genomic DNA characterisation of Leishmania." Thesis, University of Cambridge, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.386245.

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Tennant, Richard Kenneth. "Genomic analysis of microfossils in lake sediments." Thesis, University of Exeter, 2015. http://hdl.handle.net/10871/20649.

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Botryococcus braunii is a microscopic, colonial green alga that may be found in fresh and brackish waters throughout the globe. B. braunii is unique in that it constitutively synthesises and secretes copious amounts of various long-chain (C23-C40) hydrocarbons, generically termed “botryococcenes”. Botryococcanes, the hydrogenated forms of botryococcenes, comprise 1% of the fossil hydrocarbons found in petroleum deposits and in oil-shales. Microfossils identified as Botryococcus by optical and scanning electron microscopy are also abundant in these strata, but the actual identity and precise re
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Fritz, Markus Hsi-Yang. "Exploiting high throughput DNA sequencing data for genomic analysis." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610819.

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Humphreys, Timothy. "Towards high efficiency microfluidic DNA extension for genomic analysis." Thesis, University of Southampton, 2011. https://eprints.soton.ac.uk/342309/.

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Genomic analysis and DNA sequencing is a mature field with many established techniques. Developments in micro- and nanofabrication over the last decade or more have brought advances in a number of areas of chemical and biological analysis and genomics has been of particular interest. This thesis presents the development of two new techniques in microfluidic DNA manipulation that are directly applicable to the fabrication of next-generation genomic analysis devices. A key area for any miniaturised device is the ‘world-to-chip’ connection. Even the most highly integrated micro total analysis sys
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Karanam, Suresh Kumar. "Automation of comparative genomic promoter analysis of DNA microarray datasets." Thesis, Available online, Georgia Institute of Technology, 2004:, 2003. http://etd.gatech.edu/theses/available/etd-04062004-164658/unrestricted/karanam%5Fsuresh%5Fk%5F200312%5Fms.pdf.

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Stranneheim, Henrik. "Enabling massive genomic and transcriptomic analysis." Doctoral thesis, KTH, Genteknologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-45957.

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In recent years there have been tremendous advances in our ability to rapidly and cost-effectively sequence DNA. This has revolutionized the fields of genetics and biology, leading to a deeper understanding of the molecular events in life processes. The rapid advances have enormously expanded sequencing opportunities and applications, but also imposed heavy strains on steps prior to sequencing, as well as the subsequent handling and analysis of the massive amounts of sequence data that are generated, in order to exploit the full capacity of these novel platforms. The work presented in this the
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Choe, Juno. "Genomic analysis by single cell flow sorting /." Thesis, Connect to this title online; UW restricted, 2003. http://hdl.handle.net/1773/10850.

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Books on the topic "Genomic DNA of E.coli analysis"

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International, Strategic Directions. Microarray technology: The next step in genomic and proteomic analysis. Strategic Directions International, 2001.

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Kasprzak, Marta. Combinatorial models and methods for reading genomic sequences. Wydawn. Politechniki Poznańskiej, 2004.

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Applying genomic and proteomic microarray technology in drug discovery. CRC Press, 2005.

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Detection of NonAmplified Genomic DNA Biological and Medical Physics Biomedical Engineering. Springer, 2012.

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Matson, Robert S. Applying Genomic and Proteomic Microarray Technology in Drug Discovery, Second Edition. Taylor & Francis Group, 2013.

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Choi, Mieyoung. Sequencing and cloning of the N4-coded single-stranded DNA binding protein gene: Identification and functional analysis of active domains. 1992.

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Abdallah, Roshan. Evaluation of DNA hybridization probes for detecting Xanthomonas campestris pv. vesicatoria and analysis of genomic diversity by RFLP techniques. 1993.

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Otwinowski, Zdzislaw. Crystal structure analysis at 1.9 Å resolution of the complex between E. coli TRP repressor and its cognate DNA sequence. 1989.

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Taberlet, Pierre, Aurélie Bonin, Lucie Zinger, and Eric Coissac. Introduction to environmental DNA (eDNA). Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198767220.003.0001.

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Chapter “Introduction to environmental DNA (eDNA)” defines the central concepts of this book. Environmental DNA (eDNA) corresponds to a mixture of genomic DNA from many different organisms found in an environmental sample such as water, soil, or feces. DNA metabarcoding can be defined as the simultaneous DNA-based identification of many taxa found in the same eDNA extract. It is usually based on the analysis of a metabarcode (i.e., a short and taxonomically informative DNA region). Metagenomics refers to the assembly and functional analysis of the different genomes found in an environmental sa
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Stauropoulos, Dimitrios James. An analysis of the interplay between telomeric factors and DNA repair proteins, in the human ALT pathway and cellular response to genomic double strand breaks. 2005.

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Book chapters on the topic "Genomic DNA of E.coli analysis"

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Cristea, P. D., and R. Tuduce. "Nucleotide Genomic Signal DNA Analysis." In IFMBE Proceedings. Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-23508-5_354.

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Li, Yuanyuan, and Trygve O. Tollefsbol. "DNA Methylation Detection: Bisulfite Genomic Sequencing Analysis." In Methods in Molecular Biology. Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-316-5_2.

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Shultzaberger, Ryan K., and John Dresios. "Identification of Genomic Alterations Through Multilevel DNA Structural Analysis." In Methods in Molecular Biology. Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8931-7_16.

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Pevsner, Jonathan. "Analysis of Genomic DNA with the UCSC Genome Browser." In Methods in Molecular Biology. Humana Press, 2009. http://dx.doi.org/10.1007/978-1-59745-251-9_14.

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An, Chung Sun, W. Stuart Riggsby, and Beth C. Mullin. "Restriction pattern analysis of genomic DNA of Frankia isolates." In Frankia and Actinorhizal Plants. Springer Netherlands, 1985. http://dx.doi.org/10.1007/978-94-009-5147-1_4.

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Shibutani, Makoto, and Chikako Uneyama. "Methacarn Fixation for Genomic DNA Analysis in Microdissected Cells." In Laser Capture Microdissection. Humana Press, 2005. http://dx.doi.org/10.1385/1-59259-853-6:011.

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Baba, Yoshinobu. "Nanochip Technology for Single DNA Molecule Analysis and Human Genomic Polymorphism Analysis." In Micro Total Analysis Systems 2000. Springer Netherlands, 2000. http://dx.doi.org/10.1007/978-94-017-2264-3_109.

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Graham, G. C., and R. J. Henry. "Preparation of Fungal Genomic DNA for PCR and RAPD Analysis." In Fingerprinting Methods Based on Arbitrarily Primed PCR. Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-642-60441-6_5.

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Jacobson, D. R., and J. N. Buxbaum. "Detection of Variant Transthyretin Genes by Restriction Analysis of PCR-Amplified Genomic DNA." In Amyloid and Amyloidosis 1990. Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-011-3284-8_160.

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Lan, Tianying, and Charlotte Lindqvist. "Paleogenomics: Genome-Scale Analysis of Ancient DNA and Population and Evolutionary Genomic Inferences." In Population Genomics. Springer International Publishing, 2018. http://dx.doi.org/10.1007/13836_2017_7.

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Conference papers on the topic "Genomic DNA of E.coli analysis"

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Yamamoto, Kaneyoshi, Tomohiro Shimada, and Akira Ishihama. "Comprehensive analysis for the recognition sequences of DNA-binding transcription factors within the E. coli genome using the newly developed "Promoter Chip"." In 2008 International Symposium on Micro-NanoMechatronics and Human Science (MHS). IEEE, 2008. http://dx.doi.org/10.1109/mhs.2008.4752468.

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Cristea, Paul Dan, and Rodica Tuduce. "Mitochondrial DNA Analysis Using Genomic Signals." In 2009 16th International Conference on Systems, Signals and Image Processing. IEEE, 2009. http://dx.doi.org/10.1109/iwssip.2009.5367711.

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Mishra, Amrita, Stacey Harper, and Soon-Il Yun. "Interaction of biosynthesized gold nanoparticles with genomic DNA isolated from E. coli and S. aureus." In 2011 IEEE 11th International Conference on Nanotechnology (IEEE-NANO). IEEE, 2011. http://dx.doi.org/10.1109/nano.2011.6144535.

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Yu, Yongkun, Na Li, and Qingpeng Sun. "Cloning and Analysis of LeWRKY2 Genomic DNA." In 2011 5th International Conference on Bioinformatics and Biomedical Engineering (iCBBE). IEEE, 2011. http://dx.doi.org/10.1109/icbbe.2011.5780144.

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Cristea, Paul Dan, and Rodica Tuduce. "Nucleotide Genomic Signal analysis of hominidae mitochondrial DNA." In 2009 16th International Conference on Digital Signal Processing (DSP). IEEE, 2009. http://dx.doi.org/10.1109/icdsp.2009.5201251.

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Chopde, Smita, and U. S. Pushpa. "Genomic analysis - reading DNA sequence and plotting sequence and condon." In 2017 International Conference on Computing Methodologies and Communication (ICCMC). IEEE, 2017. http://dx.doi.org/10.1109/iccmc.2017.8282534.

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Sun Qingpeng and Yu Yongkun. "Molecular cloning and bioinformatics analysis of genomic DNA of LeWRKY1." In 2010 2nd International Conference on Information Science and Engineering (ICISE). IEEE, 2010. http://dx.doi.org/10.1109/icise.2010.5690845.

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Joe, Soobok, and Hojung Nam. "Identification of a Specific Base Sequence of Pathogenic E. Coli through a Genomic Analysis." In the ACM 8th International Workshop. ACM Press, 2014. http://dx.doi.org/10.1145/2665970.2665981.

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Wu, Yongzhong, Stephen L. Wang, Smitha Antony, et al. "Abstract 1755: E. coli genomic DNA fragments induce cGAS-STING-mediated DUOX2 expression in human pancreatic cancer cells that is associated with H2O2-related DNA damage." In Proceedings: AACR Annual Meeting 2021; April 10-15, 2021 and May 17-21, 2021; Philadelphia, PA. American Association for Cancer Research, 2021. http://dx.doi.org/10.1158/1538-7445.am2021-1755.

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Tao, Jun, Yan Wang, Li Wen, Zhicheng Wang, and Bi-Jun Tan. "Cloning and Bioinformatics Analysis of Genomic DNA Sequences of Gastrodia Tuber." In 2009 3rd International Conference on Bioinformatics and Biomedical Engineering (iCBBE). IEEE, 2009. http://dx.doi.org/10.1109/icbbe.2009.5162508.

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Reports on the topic "Genomic DNA of E.coli analysis"

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Nyberg, Kara A., and Ted A. Weinert. Analysis of Rad9 Functions; Roles in the Checkpoint Response, DNA Damage Processing, and Prevention of Genomic Instability. Defense Technical Information Center, 2003. http://dx.doi.org/10.21236/ada418042.

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Lerman, L. S. [Cloning-idependent mapping technology for genomic fidelity, contig linking, C-DNA site analysis, and gene detection]. Final report. Office of Scientific and Technical Information (OSTI), 1994. http://dx.doi.org/10.2172/10111141.

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