Journal articles: 'DNA - Data processing'

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Belov, D. A., Yu V. Belov, and V. V. Manoylov. "DNA MELTING DATA PROCESSING TECHNIQUES DEVELOPMENT." NAUCHNOE PRIBOROSTROENIE 27, no. 1 (February 28, 2017): 83–89. http://dx.doi.org/10.18358/np-27-1-i8389.

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Wendl, M. C., I. Korf, A. T. Chinwalla, and L. W. Hillier. "Automated processing of raw DNA sequence data." IEEE Engineering in Medicine and Biology Magazine 20, no. 4 (2001): 41–48. http://dx.doi.org/10.1109/51.940044.

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Ghoneimy, Samy, and Samir Abou El-Seoud. "A MapReduce Framework for DNA Sequencing Data Processing." International Journal of Recent Contributions from Engineering, Science & IT (iJES) 4, no. 4 (December 30, 2016): 11. http://dx.doi.org/10.3991/ijes.v4i4.6537.

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Genomics and Next Generation Sequencers (NGS) like Illumina Hiseq produce data in the order of ‎‎200 billion base pairs in a single one-week run for a 60x human genome coverage, which ‎requires modern high-throughput experimental technologies that can ‎only be tackled with high performance computing (HPC) and specialized software algorithms called ‎‎“short read aligners”. This paper focuses on the implementation of the DNA sequencing as a set of MapReduce programs that will accept a DNA data set as a FASTQ file and finally generate a VCF (variant call format) file, which has variants for a given DNA data set. In this paper MapReduce/Hadoop along with Burrows-Wheeler Aligner (BWA), Sequence Alignment/Map (SAM) ‎tools, are fully utilized to provide various utilities for manipulating alignments, including sorting, merging, indexing, ‎and generating alignments. The Map-Sort-Reduce process is designed to be suited for a Hadoop framework in ‎which each cluster is a traditional N-node Hadoop cluster to utilize all of the Hadoop features like HDFS, program ‎management and fault tolerance. The Map step performs multiple instances of the short read alignment algorithm ‎‎(BoWTie) that run in parallel in Hadoop. The ordered list of the sequence reads are used as input tuples and the ‎output tuples are the alignments of the short reads. In the Reduce step many parallel instances of the Short ‎Oligonucleotide Analysis Package for SNP (SOAPsnp) algorithm run in the cluster. Input tuples are sorted ‎alignments for a partition and the output tuples are SNP calls. Results are stored via HDFS, and then archived in ‎SOAPsnp format. ‎ The proposed framework enables extremely fast discovering somatic mutations, inferring population genetical ‎parameters, and performing association tests directly based on sequencing data without explicit genotyping or ‎linkage-based imputation. It also demonstrate that this method achieves comparable accuracy to alternative ‎methods for sequencing data processing.‎‎

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Bei barth, T., K. Fellenberg, B. Brors, R. Arribas-Prat, J. M. Boer, N. C. Hauser, M. Scheideler, et al. "Processing and quality control of DNA array hybridization data." Bioinformatics 16, no. 11 (November 1, 2000): 1014–22. http://dx.doi.org/10.1093/bioinformatics/16.11.1014.

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Mendizabal-Ruiz, Gerardo, Israel Román-Godínez, Sulema Torres-Ramos, Ricardo A. Salido-Ruiz, Hugo Vélez-Pérez, and J. Alejandro Morales. "Genomic signal processing for DNA sequence clustering." PeerJ 6 (January 24, 2018): e4264. http://dx.doi.org/10.7717/peerj.4264.

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Genomic signal processing (GSP) methods which convert DNA data to numerical values have recently been proposed, which would offer the opportunity of employing existing digital signal processing methods for genomic data. One of the most used methods for exploring data is cluster analysis which refers to the unsupervised classification of patterns in data. In this paper, we propose a novel approach for performing cluster analysis of DNA sequences that is based on the use of GSP methods and the K-means algorithm. We also propose a visualization method that facilitates the easy inspection and analysis of the results and possible hidden behaviors. Our results support the feasibility of employing the proposed method to find and easily visualize interesting features of sets of DNA data.

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WANG, Ting-Zhang, Gao SHAN, Jian-Hong XU, and Qing-Zhong XUE. "Genome-scale sequence data processing and epigenetic analysis of DNA methylation." Hereditas (Beijing) 35, no. 6 (September 29, 2013): 685–94. http://dx.doi.org/10.3724/sp.j.1005.2013.00685.

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Wilhelm-Benartzi, C. S., D. C. Koestler, M. R. Karagas, J. M. Flanagan, B. C. Christensen, K. T. Kelsey, C. J. Marsit, E. A. Houseman, and R. Brown. "Review of processing and analysis methods for DNA methylation array data." British Journal of Cancer 109, no. 6 (August 27, 2013): 1394–402. http://dx.doi.org/10.1038/bjc.2013.496.

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Merkel, Angelika, Marcos Fernández-Callejo, Eloi Casals, Santiago Marco-Sola, Ronald Schuyler, Ivo G. Gut, and Simon C. Heath. "gemBS: high throughput processing for DNA methylation data from bisulfite sequencing." Bioinformatics 35, no. 5 (August 21, 2018): 737–42. http://dx.doi.org/10.1093/bioinformatics/bty690.

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Nersisyan, Stepan, Maxim Shkurnikov, Andrey Poloznikov, Andrey Turchinovich, Barbara Burwinkel, Nikita Anisimov, and Alexander Tonevitsky. "A Post-Processing Algorithm for miRNA Microarray Data." International Journal of Molecular Sciences 21, no. 4 (February 12, 2020): 1228. http://dx.doi.org/10.3390/ijms21041228.

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One of the main disadvantages of using DNA microarrays for miRNA expression profiling is the inability of adequate comparison of expression values across different miRNAs. This leads to a large amount of miRNAs with high scores which are actually not expressed in examined samples, i.e., false positives. We propose a post-processing algorithm which performs scoring of miRNAs in the results of microarray analysis based on expression values, time of discovery of miRNA, and correlation level between the expressions of miRNA and corresponding pre-miRNA in considered samples. The algorithm was successfully validated by the comparison of the results of its application to miRNA microarray breast tumor samples with publicly available miRNA-seq breast tumor data. Additionally, we obtained possible reasons why miRNA can appear as a false positive in microarray study using paired miRNA sequencing and array data. The use of DNA microarrays for estimating miRNA expression profile is limited by several factors. One of them consists of problems with comparing expression values of different miRNAs. In this work, we show that situation can be significantly improved if some additional information is taken into consideration in a comparison.

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Hutchinson, Franklin. "Use of data from bacteria to interpret data on DNA damage processing in mammalian cells." Mutation Research/Reviews in Genetic Toxicology 220, no. 2-3 (March 1989): 269–78. http://dx.doi.org/10.1016/0165-1110(89)90031-6.

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Garzon, Max H., Kiran C. Bobba, Andrew Neel, and Vinhthuy Phan. "DNA-Based Indexing." International Journal of Nanotechnology and Molecular Computation 2, no. 3 (July 2010): 25–45. http://dx.doi.org/10.4018/jnmc.2010070102.

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DNA has been acknowledged as a suitable medium for massively parallel computing and as a “smart” glue for self-assembly. In this paper, a third capability of DNA is described in detail as memory capable of encoding and processing large amounts of data so that information can be retrieved associatively based on content. The technique is based on a novel representation of data on DNA that can shed information on the way DNA-, RNA- and other biomolecules encode information, which may be potentially important in applications to fields like bioinformatics and genetics, and natural language processing. Analyses are also provided of the sensitivity, robustness, and bounds on the theoretical capacity of the memories. Finally, the potential use of the memories are illustrated with two applications, one in genomic analysis for identification and classification, another in information retrieval from text data in abiotic form.

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Levy, Dan, Mariel Vazquez, Michael Cornforth, Bradford Loucas, Rainer K. Sachs, and Javier Arsuaga. "Comparing DNA Damage-Processing Pathways by Computer Analysis of Chromosome Painting Data." Journal of Computational Biology 11, no. 4 (August 2004): 626–41. http://dx.doi.org/10.1089/cmb.2004.11.626.

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Sun, Ming-an, Karthik Raja Velmurugan, David Keimig, and Hehuang Xie. "HBS-Tools for Hairpin Bisulfite Sequencing Data Processing and Analysis." Advances in Bioinformatics 2015 (December 20, 2015): 1–4. http://dx.doi.org/10.1155/2015/760423.

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The emerging genome-wide hairpin bisulfite sequencing (hairpin-BS-Seq) technique enables the determination of the methylation pattern for DNA double strands simultaneously. Compared with traditional bisulfite sequencing (BS-Seq) techniques, hairpin-BS-Seq can determine methylation fidelity and increase mapping efficiency. However, no computational tool has been designed for the analysis of hairpin-BS-Seq data yet. Here we present HBS-tools, a set of command line based tools for the preprocessing, mapping, methylation calling, and summarizing of genome-wide hairpin-BS-Seq data. It accepts paired-end hairpin-BS-Seq reads to recover the original (pre-bisulfite-converted) sequences using global alignment and then calls the methylation statuses for cytosines on both DNA strands after mapping the original sequences to the reference genome. After applying to hairpin-BS-Seq datasets, we found that HBS-tools have a reduced mapping time and improved mapping efficiency compared with state-of-the-art mapping tools. The HBS-tools source scripts, along with user guide and testing data, are freely available for download.

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Hansson, O., and L. Albinsson. "Automatic data processing of reference DNA-profiles from FTA and non-FTA samples." Forensic Science International: Genetics Supplement Series 1, no. 1 (August 2008): 29–31. http://dx.doi.org/10.1016/j.fsigss.2007.10.143.

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Yang, Yunfeng, Mengxia Zhu, Liyou Wu, and Jizhong Zhou. "Assessment of data processing to improve reliability of microarray experiments using genomic DNA reference." BMC Genomics 9, Suppl 2 (2008): S5. http://dx.doi.org/10.1186/1471-2164-9-s2-s5.

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Rulik, Björn, Jonas Eberle, Laura Mark, Jana Thormann, Manfred Jung, Frank Köhler, Wolfgang Apfel, et al. "Using taxonomic consistency with semi‐automated data pre‐processing for high quality DNA barcodes." Methods in Ecology and Evolution 8, no. 12 (June 29, 2017): 1878–87. http://dx.doi.org/10.1111/2041-210x.12824.

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Shapovalova, V. V., S. P. Radko, K. G. Ptitsyn, G. S. Krasnov, K. V. Nakhod, O. S. Konash, M. A. Vinogradina, E. A. Ponomarenko, D. S. Druzhilovskiy, and A. V. Lisitsa. "Processing Oxford Nanopore Long Reads Using Amazon Web Services." Biomedical Chemistry: Research and Methods 3, no. 4 (2020): e00131. http://dx.doi.org/10.18097/bmcrm00131.

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Studies of genomes and transcriptomes are performed using sequencers that read the sequence of nucleotide residues of genomic DNA, RNA, or complementary DNA (cDNA). The analysis consists of an experimental part (obtaining primary data) and bioinformatic processing of primary data. The bioinformatics part is performed with different sets of input parameters. The selection of the optimal values of the parameters, as a rule, requires significant computing power. The article describes a protocol for processing transcriptome data by virtual computers provided by the cloud platform Amazon Web Services (AWS) using the example of the recently emerging technology of long DNA and RNA sequences (Oxford Nanopore Technology). As a result, a virtual machine and instructions for its use have been developed, thus allowing a wide range of molecular biologists to independently process the results obtained using the "Oxford nanopore".

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Luo, Yunhai, Benjamin C. Hitz, Idan Gabdank, Jason A. Hilton, Meenakshi S. Kagda, Bonita Lam, Zachary Myers, et al. "New developments on the Encyclopedia of DNA Elements (ENCODE) data portal." Nucleic Acids Research 48, no. D1 (November 12, 2019): D882—D889. http://dx.doi.org/10.1093/nar/gkz1062.

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Abstract The Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative research project aimed at identifying all the functional elements in the human and mouse genomes. Data generated by the ENCODE consortium are freely accessible at the ENCODE portal (https://www.encodeproject.org/), which is developed and maintained by the ENCODE Data Coordinating Center (DCC). Since the initial portal release in 2013, the ENCODE DCC has updated the portal to make ENCODE data more findable, accessible, interoperable and reusable. Here, we report on recent updates, including new ENCODE data and assays, ENCODE uniform data processing pipelines, new visualization tools, a dataset cart feature, unrestricted public access to ENCODE data on the cloud (Amazon Web Services open data registry, https://registry.opendata.aws/encode-project/) and more comprehensive tutorials and documentation.

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Herlin, Paulette, David Deman, Christophe Boudry, Francois Angot, and Francoise Duigou. "Image Galleries for DNA Ploidy Measurement: a Tool for Screening, Learning, Data and Image Processing." Microscopy Microanalysis Microstructures 7, no. 5-6 (1996): 355–60. http://dx.doi.org/10.1051/mmm:1996133.

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Najam, Maleeha, Raihan Ur Rasool, Hafiz Farooq Ahmad, Usman Ashraf, and Asad Waqar Malik. "Pattern Matching for DNA Sequencing Data Using Multiple Bloom Filters." BioMed Research International 2019 (April 14, 2019): 1–9. http://dx.doi.org/10.1155/2019/7074387.

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Storing and processing of large DNA sequences has always been a major problem due to increasing volume of DNA sequence data. However, a number of solutions have been proposed but they require significant computation and memory. Therefore, an efficient storage and pattern matching solution is required for DNA sequencing data. Bloom filters (BFs) represent an efficient data structure, which is mostly used in the domain of bioinformatics for classification of DNA sequences. In this paper, we explore more dimensions where BFs can be used other than classification. A proposed solution is based on Multiple Bloom Filters (MBFs) that finds all the locations and number of repetitions of the specified pattern inside a DNA sequence. Both of these factors are extremely important in determining the type and intensity of any disease. This paper serves as a first effort towards optimizing the search for location and frequency of substrings in DNA sequences using MBFs. We expect that further optimizations in the proposed solution can bring remarkable results as this paper presents a proof of concept implementation for a given set of data using proposed MBFs technique. Performance evaluation shows improved accuracy and time efficiency of the proposed approach.

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Muñoz-Minjares, J. U., Yuriy S. Shmaliy, and Tatiana G. Popova. "Critical evaluation of CNA estimators for DNA data using matching confidence masks and WGS technology." Biomedical Signal Processing and Control 70 (September 2021): 103004. http://dx.doi.org/10.1016/j.bspc.2021.103004.

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Wang, Renjing, Nicole S. Persky, Barney Yoo, Ouathek Ouerfelli, Agata Smogorzewska, Stephen J. Elledge, and Nikola P. Pavletich. "Mechanism of DNA interstrand cross-link processing by repair nuclease FAN1." Science 346, no. 6213 (November 27, 2014): 1127–30. http://dx.doi.org/10.1126/science.1258973.

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DNA interstrand cross-links (ICLs) are highly toxic lesions associated with cancer and degenerative diseases. ICLs can be repaired by the Fanconi anemia (FA) pathway and through FA-independent processes involving the FAN1 nuclease. In this work, FAN1-DNA crystal structures and biochemical data reveal that human FAN1 cleaves DNA successively at every third nucleotide. In vitro, this exonuclease mechanism allows FAN1 to excise an ICL from one strand through flanking incisions. DNA access requires a 5′-terminal phosphate anchor at a nick or a 1- or 2-nucleotide flap and is augmented by a 3′ flap, suggesting that FAN1 action is coupled to DNA synthesis or recombination. FAN1’s mechanism of ICL excision is well suited for processing other localized DNA adducts as well.

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Jurga, Anna, and Jakub Mondzelewski. "Functioning of DNA Database in Poland." Issues of Forensic Science 297 (2017): 59–65. http://dx.doi.org/10.34836/pk.2017.297.2.

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Forensic DNA databases that operate in the zone forming an interface between science and law have the purpose of gathering and processing DNA profiles for the needs of law enforcement and judicial authorities responsible for preventing and combating crime. Therefore, their appropriate functioning is important. On one hand, it improves efficiency of police work and, on the other hand, it has to play a required role in protecting citizen rights and personal data. The National DNA Database has functioned in Poland since 2007. Its effectiveness is correlated with the number of stored profiles. Despite small collection the Database has on numerous occasions proven its high usefulness in solving criminal cases. The possibility of carrying out searches in other countries databases, as well as legislative and organisational undertakings aiming at improvement of the Database operation are gradually bringing effects and result in an increased detective potential of this tool.

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El-Seoud, Samir Abou, Reham Fouad Mohamed, and Samy Ghoneimy. "DNA Computing: Challenges and Application." International Journal of Interactive Mobile Technologies (iJIM) 11, no. 2 (April 11, 2017): 74. http://dx.doi.org/10.3991/ijim.v11i2.6564.

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Much of our scientific, technological, and economic future depends on the availability of an ever-increasing supply of computational power. However, the increasing demand for such power has pushed electronic technology to the limit of physical feasibility and has raised the concern that this technology may not be able to sustain our growth in the near future. It became important to consider an alternative means of achieving computational power. In this regard, DNA computing was introduced based on the usage of DNA and molecular biology hardware instead of the typical silicon based technology. The molecular computers could take advantage of DNA's physical properties to store information and perform calculations. These include extremely dense information storage, enormous parallelism and extraordinary energy efficiency. One of the main advantages that DNA computations would add to computation is its self - parallel processing while most of the electronic computers now use linear processing. In this paper, the DNA computation is reviewed and its state of the art challenges and applications are presented. Some of these applications are those require fast processing, at which DNA computers would be able to solve the hardest problems faster than the traditional ones. For example, 10 trillion DNA molecules can fit in one cubic centimeter that would result in a computer that holds 10 terabytes of data. Moreover, this work focuses on whether a large scale molecular computer can be built.

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Yang, Lin. "The Research and Application of Forensic DNA Fragment Analysis Software." Applied Mechanics and Materials 687-691 (November 2014): 1904–7. http://dx.doi.org/10.4028/www.scientific.net/amm.687-691.1904.

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Forensic DNA analysis software is dedicated with forensic DNA testing platform matching data analysis tools, which can realize the platform acquisition, pretreatment of DNA data analysis and deep processing. It realizes the automation of forensic DNA testing process, further to get rid of dependence on foreign analysis software of DNA testing technology in China. It has a good prospect of popularization and application.

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Lieljuksis, Aldis. "THE PROBLEMS OF OBTAINING AND PROCESSING DNA SAMPLES IN CRIMINAL PROCEEDINGS." Administrative and Criminal Justice 1, no. 74 (June 30, 2016): 38. http://dx.doi.org/10.17770/acj.v1i74.2883.

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The article deals with the issue raised in the society regarding constitutional complaint a submitted to the Constitutional Court against the national DNA database and the compliance of the legal norms with Section 96 of the Satversme. The author of the article writes about the issues related to the legal framework of DNA and biometric data sampling from suspects in the context of the EP Resolution No. 2008/615 / JHA, the requirements of the ECHR and the Estonian Criminal procedure regulation. In conclusion, the author is of the opinion that the current DNA sampling legislation does not provide many options for process facilitator and DNA samples must be obtained from all suspected persons to whom such status is applied regardless of the qualification of the offence and the need for criminal proceedings.

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Mills, Nicholas, Ethan M. Bensman, William L. Poehlman, Walter B. Ligon, and F. Alex Feltus. "Moving Just Enough Deep Sequencing Data to Get the Job Done." Bioinformatics and Biology Insights 13 (January 2019): 117793221985635. http://dx.doi.org/10.1177/1177932219856359.

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Motivation: As the size of high-throughput DNA sequence datasets continues to grow, the cost of transferring and storing the datasets may prevent their processing in all but the largest data centers or commercial cloud providers. To lower this cost, it should be possible to process only a subset of the original data while still preserving the biological information of interest. Results: Using 4 high-throughput DNA sequence datasets of differing sequencing depth from 2 species as use cases, we demonstrate the effect of processing partial datasets on the number of detected RNA transcripts using an RNA-Seq workflow. We used transcript detection to decide on a cutoff point. We then physically transferred the minimal partial dataset and compared with the transfer of the full dataset, which showed a reduction of approximately 25% in the total transfer time. These results suggest that as sequencing datasets get larger, one way to speed up analysis is to simply transfer the minimal amount of data that still sufficiently detects biological signal. Availability: All results were generated using public datasets from NCBI and publicly available open source software.

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Gururaj T. and Siddesh G. M. "Hybrid Approach for Enhancing Performance of Genomic Data for Stream Matching." International Journal of Cognitive Informatics and Natural Intelligence 15, no. 4 (October 2021): 1–18. http://dx.doi.org/10.4018/ijcini.20211001.oa38.

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In gene expression analysis, the expression levels of thousands of genes are analyzed, such as separate stages of treatments or diseases. Identifying particular gene sequence pattern is a challenging task with respect to performance issues. The proposed solution addresses the performance issues in genomic stream matching by involving assembly and sequencing. Counting the k-mer based on k-input value and while performing DNA sequencing tasks, the researches need to concentrate on sequence matching. The proposed solution addresses performance issue metrics such as processing time for k-mer counting, number of operations for matching similarity, memory utilization while performing similarity search, and processing time for stream matching. By suggesting an improved algorithm, Revised Rabin Karp(RRK) for basic operation and also to achieve more efficiency, the proposed solution suggests a novel framework based on Hadoop MapReduce blended with Pig & Apache Tez. The measure of memory utilization and processing time proposed model proves its efficiency when compared to existing approaches.

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Farkaš, Tomáš, Jozef Sitarčík, Broňa Brejová, and Mária Lucká. "SWSPM: A Novel Alignment-Free DNA Comparison Method Based on Signal Processing Approaches." Evolutionary Bioinformatics 15 (January 2019): 117693431984907. http://dx.doi.org/10.1177/1176934319849071.

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Computing similarity between 2 nucleotide sequences is one of the fundamental problems in bioinformatics. Current methods are based mainly on 2 major approaches: (1) sequence alignment, which is computationally expensive, and (2) faster, but less accurate, alignment-free methods based on various statistical summaries, for example, short word counts. We propose a new distance measure based on mathematical transforms from the domain of signal processing. To tolerate large-scale rearrangements in the sequences, the transform is computed across sliding windows. We compare our method on several data sets with current state-of-art alignment-free methods. Our method compares favorably in terms of accuracy and outperforms other methods in running time and memory requirements. In addition, it is massively scalable up to dozens of processing units without the loss of performance due to communication overhead. Source files and sample data are available at https://bitbucket.org/fiitstubioinfo/swspm/src

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Feltus, Frank A., Joseph R. Breen, Juan Deng, Ryan S. Izard, Christopher A. Konger, Walter B. Ligon, Don Preuss, and Kuang-Ching Wang. "The Widening Gulf between Genomics Data Generation and Consumption: A Practical Guide to Big Data Transfer Technology." Bioinformatics and Biology Insights 9s1 (January 2015): BBI.S28988. http://dx.doi.org/10.4137/bbi.s28988.

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In the last decade, high-throughput DNA sequencing has become a disruptive technology and pushed the life sciences into a distributed ecosystem of sequence data producers and consumers. Given the power of genomics and declining sequencing costs, biology is an emerging “Big Data” discipline that will soon enter the exabyte data range when all subdisciplines are combined. These datasets must be transferred across commercial and research networks in creative ways since sending data without thought can have serious consequences on data processing time frames. Thus, it is imperative that biologists, bioinformaticians, and information technology engineers recalibrate data processing paradigms to fit this emerging reality. This review attempts to provide a snapshot of Big Data transfer across networks, which is often overlooked by many biologists. Specifically, we discuss four key areas: 1) data transfer networks, protocols, and applications; 2) data transfer security including encryption, access, firewalls, and the Science DMZ; 3) data flow control with software-defined networking; and 4) data storage, staging, archiving and access. A primary intention of this article is to orient the biologist in key aspects of the data transfer process in order to frame their genomics-oriented needs to enterprise IT professionals.

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Xu, Naihan, Nadia Hegarat, Elizabeth J. Black, Mary T. Scott, Helfrid Hochegger, and David A. Gillespie. "Akt/PKB suppresses DNA damage processing and checkpoint activation in late G2." Journal of Cell Biology 190, no. 3 (August 2, 2010): 297–305. http://dx.doi.org/10.1083/jcb.201003004.

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Using chemical genetics to reversibly inhibit Cdk1, we find that cells arrested in late G2 are unable to delay mitotic entry after irradiation. Late G2 cells detect DNA damage lesions and form γ-H2AX foci but fail to activate Chk1. This reflects a lack of DNA double-strand break processing because late G2 cells fail to recruit RPA (replication protein A), ATR (ataxia telangiectasia and Rad3 related), Rad51, or CtIP (C-terminal interacting protein) to sites of radiation-induced damage, events essential for both checkpoint activation and initiation of DNA repair by homologous recombination. Remarkably, inhibition of Akt/PKB (protein kinase B) restores DNA damage processing and Chk1 activation after irradiation in late G2. These data demonstrate a previously unrecognized role for Akt in cell cycle regulation of DNA repair and checkpoint activation. Because Akt/PKB is frequently activated in many tumor types, these findings have important implications for the evolution and therapy of such cancers.

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Brodzik, A. K. "Phase-only filtering for the masses (of DNA Data): a new approach to sequence alignment." IEEE Transactions on Signal Processing 54, no. 6 (June 2006): 2456–66. http://dx.doi.org/10.1109/tsp.2006.873717.

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Mihajlovic, Sanja, Silvia Lang, Marta V. Sut, Heimo Strohmaier, Christian J. Gruber, Günther Koraimann, Elena Cabezón, Gabriel Moncalián, Fernando de la Cruz, and Ellen L. Zechner. "Plasmid R1 Conjugative DNA Processing Is Regulated at the Coupling Protein Interface." Journal of Bacteriology 191, no. 22 (September 18, 2009): 6877–87. http://dx.doi.org/10.1128/jb.00918-09.

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ABSTRACT Selective substrate uptake controls initiation of macromolecular secretion by type IV secretion systems in gram-negative bacteria. Type IV coupling proteins (T4CPs) are essential, but the molecular mechanisms governing substrate entry to the translocation pathway remain obscure. We report a biochemical approach to reconstitute a regulatory interface between the plasmid R1 T4CP and the nucleoprotein relaxosome dedicated to the initiation stage of plasmid DNA processing and substrate presentation. The predicted cytosolic domain of T4CP TraD was purified in a predominantly monomeric form, and potential regulatory effects of this protein on catalytic activities exhibited by the relaxosome during transfer initiation were analyzed in vitro. TraDΔN130 stimulated the TraI DNA transesterase activity apparently via interactions on both the protein and the DNA levels. TraM, a protein interaction partner of TraD, also increased DNA transesterase activity in vitro. The mechanism may involve altered DNA conformation as TraM induced underwinding of oriT plasmid DNA in vivo (ΔLk = −4). Permanganate mapping of the positions of duplex melting due to relaxosome assembly with TraDΔN130 on supercoiled DNA in vitro confirmed localized unwinding at nic but ruled out formation of an open complex compatible with initiation of the TraI helicase activity. These data link relaxosome regulation to the T4CP and support the model that a committed step in the initiation of DNA export requires activation of TraI helicase loading or catalysis.

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Paliwal, Kuldip K., and Alok Sharma. "Improved direct LDA and its application to DNA microarray gene expression data." Pattern Recognition Letters 31, no. 16 (December 2010): 2489–92. http://dx.doi.org/10.1016/j.patrec.2010.08.003.

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Díaz-Valdés, Nancy, Miguel A. Comendador, and L. María Sierra. "Mus308 Processes Oxygen and Nitrogen Ethylation DNA Damage in Germ Cells of Drosophila." Journal of Nucleic Acids 2010 (2010): 1–7. http://dx.doi.org/10.4061/2010/416364.

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TheD. melanogaster mus308gene, highly conserved among higher eukaryotes, is implicated in the repair of cross-links and of O-ethylpyrimidine DNA damage, working in a DNA damage tolerance mechanism. However, despite its relevance, its possible role on the processing of different DNA ethylation damages is not clear. To obtain data on mutation frequency and on mutation spectra inmus308deficient (mus308-) conditions, the ethylating agent diethyl sulfate (DES) was analysed in postmeiotic male germ cells. These data were compared with those corresponding tomus308efficient conditions. Our results indicate that Mus308 is necessary for the processing of oxygen and N-ethylation damage, for the survival of fertilized eggs depending on the level of induced DNA damage, and for an influence of the DNA damage neighbouring sequence. These results support the role ofmus308in a tolerance mechanism linked to a translesion synthesis pathway and also to the alternative end-joinig system.

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Bharne, Dhammapal, Praveen Kant, and Vaibhav Vindal. "maGUI: A Graphical User Interface for Analysis and Annotation of DNA Microarray Data." Open Bioinformatics Journal 12, no. 1 (June 30, 2019): 40–44. http://dx.doi.org/10.2174/1875036201912010040.

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Summary: maGUI is a graphical user interface designed to analyze microarray data produced from experiments performed on various platforms such as Affymetrix, Agilent, Illumina, and Nimblegen and so on, automatically. It follows an integrated workflow for pre-processing and analysis of the microarray data. The user may proceed from loading of microarray data to normalization, quality check, filtering, differential gene expression, principal component analysis, clustering and classification. It also provides miscellaneous applications such as gene set test and enrichment analysis for identifying gene symbols using Bioconductor packages. Further, the user can build a co-expression network for differentially expressed genes. Tables and figures generated during the analysis can be viewed and exported to local disks. The graphical user interface is very friendly especially for the biologists to perform the most microarray data analyses and annotations without much need of learning R command line programming. Availability and Implementation: maGUI is an R package which can be downloaded freely from Comprehensive R Archive Network resource. It can be installed in any R environment with version 3.0.2 or above.

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Аулов, В. А., and V. A. Aulov. "Integration of Heterogeneous Computing Infrastructures for Genome Sequencing Data Analysis." Mathematical Biology and Bioinformatics 11, no. 2 (October 21, 2016): 205–13. http://dx.doi.org/10.17537/2016.11.205.

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Recent technological achievements in Next Generation Sequencing (NGS) lead to significant increase in amounts of data which must be processed, analyzed and made remotely available to scientists. This, in turn, increased the requirements to the computing platforms used for data processing in terms of RAM and processors’ power. Entirely new approaches in organization of computations are required in order to process data efficiently. Authors of this paper have researched the possibility of adapting the methods and approaches employed in high energy physics for integration of heterogeneous computing resources into unified computing platform. Fully specified data and task management system based on computing resources of National Research Centre “Kurchatov Institute” was developed. We’ve also developed a workflow for processing genome sequencing data with PALEOMIX package and integrated it into the system. Results of the developed system’s approbation on ancient mammoth DNA sequencing task have demonstrated a significant reduction in total computational time of the task.

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Duxin, Julien P., Benjamin Dao, Peter Martinsson, Nina Rajala, Lionel Guittat, Judith L. Campbell, Johannes N. Spelbrink, and Sheila A. Stewart. "Human Dna2 Is a Nuclear and Mitochondrial DNA Maintenance Protein." Molecular and Cellular Biology 29, no. 15 (June 1, 2009): 4274–82. http://dx.doi.org/10.1128/mcb.01834-08.

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ABSTRACT Dna2 is a highly conserved helicase/nuclease that in yeast participates in Okazaki fragment processing, DNA repair, and telomere maintenance. Here, we investigated the biological function of human Dna2 (hDna2). Immunofluorescence and biochemical fractionation studies demonstrated that hDna2 was present in both the nucleus and the mitochondria. Analysis of mitochondrial hDna2 revealed that it colocalized with a subfraction of DNA-containing mitochondrial nucleoids in unperturbed cells. Upon the expression of disease-associated mutant forms of the mitochondrial Twinkle helicase which induce DNA replication pausing/stalling, hDna2 accumulated within nucleoids. RNA interference-mediated depletion of hDna2 led to a modest decrease in mitochondrial DNA replication intermediates and inefficient repair of damaged mitochondrial DNA. Importantly, hDna2 depletion also resulted in the appearance of aneuploid cells and the formation of internuclear chromatin bridges, indicating that nuclear hDna2 plays a role in genomic DNA stability. Together, our data indicate that hDna2 is similar to its yeast counterpart and is a new addition to the growing list of proteins that participate in both nuclear and mitochondrial DNA maintenance.

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Wilk, Dariusz. "FORENSIC DATABASES IN POLAND. LEGAL ISSUES RELATED TO RIGHT TO THE PROTECTION OF PERSONAL DATA AND RIGHT TO PRIVACY." Criminalistics and Forensics, no. 66 (2021): 285–305. http://dx.doi.org/10.33994/kndise.2021.66.23.

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Forensic databases are crucial resources in criminal justice systems, which allow for detection and identification of offenders. General Data Protection Regulation and Police Directive about processing of personal data were enacted in the European Union in 2016, which implied changes in national law and policy in processing genetic and biometric data by law enforcements. Therefore, current development of DNA and fingerprint databases in Poland were revealed and compared to other European countries. Changes in the law related to processing of genetic and biometric data were analysed. Issues related to the distinction between different categories of data subject and retention time of personal data were especially commented in the view of right to the protection of personal data and right to privacy.

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Sala, Claudia, Pietro Di Lena, Danielle Fernandes Durso, Andrea Prodi, Gastone Castellani, and Christine Nardini. "Evaluation of pre-processing on the meta-analysis of DNA methylation data from the Illumina HumanMethylation450 BeadChip platform." PLOS ONE 15, no. 3 (March 10, 2020): e0229763. http://dx.doi.org/10.1371/journal.pone.0229763.

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Harbord, Kristi. "Genetic Data Privacy Solutions in the GDPR." Texas A&M Law Review 7, no. 1 (October 2019): 269–97. http://dx.doi.org/10.37419/lr.v7.i1.6.

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The intersection of healthcare and technology is a rapidly growing area. One thriving field at this intersection involves obtaining, processing, and storing genetic data. While the benefits have been great, genetic information can reveal a great deal about individuals and their families. And the information that can be conveyed from genetic data appears limitless and is constantly growing and changing. Many entities have begun storing, processing, and sharing genetic data on a very large scale. This creates many privacy concerns that the current regulatory framework does not account for. The line between patient data and consumer data is blurred; many entities are interested in obtaining genetic data with varied interests. In the direct-to-consumer genetic testing market, consumers pay to send private companies their DNA samples in exchange for a trivial amount of information about their ancestry and health risks. But health data obtained and processed by a company are subjected to far less stringent privacy regulations than health data obtained and processed at a doctor’s office or hospital. This Comment summarizes some of the current genetic privacy problems in United States laws and examines the EU’s recently adopted GDPR for a possible solution. A GDPR-style regulation could provide more consistency, give individuals more control, and protect against future unknown uses.

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Sprindzuk, M. V., L. P. Titov, and A. P. Konchits. "Сhallenging Questions of Development and Application of DNA Banks for the Purposes of Criminology and Related Disciplines." Digital Transformation, no. 1 (May 5, 2019): 49–59. http://dx.doi.org/10.38086/2522-9613-2019-1-49-59.

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Review article presents essential information on DNA databases, forensic genomics for human identification and suspect characteristics. Author reports the essential information on the topic of forensic DNA databases and data processing. DNA databases are important tools for the improvement of performance of the security organizations and services with a final goal of national security enhancement.

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Fenollar-Ferrer, C., V. Carnevale, S. Raugei, and P. Carloni. "HIV-1 Integrase–DNA Interactions Investigated by Molecular Modelling." Computational and Mathematical Methods in Medicine 9, no. 3-4 (2008): 231–43. http://dx.doi.org/10.1080/17486700802167918.

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HIV-1 integrase is the viral enzyme responsible for the insertion of the viral DNA into the host cell chromosome. This process occurs through two distinct biochemical reactions: the 3′-processing of the viral DNA and the transesterification reaction. Because experimental structural information on the reaction intermediate is not available, several molecular models have been developed. Unfortunately, none of the models of the enzyme–substrate complex is fully consistent with the available molecular biological data. We have constructed a new theoretical model based on mutagenesis experiments and cross-linking data, using a relatively accurate computational setup. The structural features of the model along with its limitations are discussed here.

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., Tin Thein Thwel, and G. R. Sinha . "Efficient Data Deduplication Mechanism for Genomic Data." CSVTU International Journal of Biotechnology Bioinformatics and Biomedical 4, no. 2 (September 3, 2019): 52–58. http://dx.doi.org/10.30732/ijbbb.20190402004.

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During the data science age, many people tend to access health concerned information and diagnosis using information technology, including telemedicine. Therefore, many researchers attempting to work with medical experts as well as bioinformatics area. In the bioinformatics field, handling the genomic data of human beings becomes essential such as collecting, storing and processing. Genomic data refers to the genome and DNA data of an organism. Unavoidably, genomic data require huge amount of storage for the customized software to analyze. Recently, genome researchers are rising the alarms over big data.This research papers attempts in significant amount of reduction of data storage by applying data deduplication process in genomic data set. Data deduplication, ‘dedupe’ in short can reduce the amount of storage because of its single instance storage nature.Therefore, data deduplication becomes one of the solutions for optimizing the huge amount of storage spaces for genome storage.We have implemented data deduplication method and applied it to genomic data and the deduplication performed successfully by using secure hash algorithm, B++ tree and sub-file level chunking algorithm. The methods were implemented in integrated approach. The files are separated into different chunks with the help of Two Threshold Two Divisors algorithm and hash function is used to get chunk identifiers. Indexing keys are constructed using the identifiersin B+ tree like index structure.Thissystem can reduce the storage space significantly when there exist duplicated data. The preliminary testing is made using NCBI datasets

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Назипова, Н. Н., and N. N. Nazipova. "Big Data in Bioinformatics." Mathematical Biology and Bioinformatics 12, no. 1 (March 10, 2017): 102–19. http://dx.doi.org/10.17537/2017.12.102.

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Sequencing of the human genome began in 1994. It took 10 years of collaborative work of many research groups from different countries in order to provide a draft of the human DNA. Modern technologies allow sequencing of a whole genome in a few days. We discuss here the advances in modern bioinformatics related to the emergence of high-performance sequencing platforms, which not only contributed to the expansion of capabilities of biology and related sciences, but also gave rise to the phenomenon of Big Data in biology. The necessity for development of new technologies and methods for organization of storage, management, analysis and visualization of big data is substantiated. Modern bioinformatics is facing not only the problem of processing enormous volumes of heterogeneous data, but also a variety of methods of interpretation and presentation of the results, the simultaneous existence of various software tools and data formats. The ways of solving the arising challenges are discussed, in particular by using experiences from other areas of modern life, such as web and business intelligence. The former is the area of scientific research and development that explores the roles and makes use of artificial intelligence and information technology (IT) for new products, services and frameworks that are empowered by the World Wide Web; the latter is the domain of IT, which addresses the issues of decision-making. New database management systems, other than relational ones, will help solve the problem of storing huge data and providing an acceptable timescale for performing search queries. New programming technologies, such as generic programming and visual programming, are designed to solve the problem of the diversity of genomic data formats and to provide the ability to quickly create one's own scripts for data processing.

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Chakrabarti, Tamal, and Devadatta Sinha. "An Efficient Technique for Finding Longest Common Subsequence of DNA Sequences." American Journal of Advanced Computing 1, no. 1 (January 1, 2020): 1–5. http://dx.doi.org/10.15864/ajac.1101.

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Molecular biologists rely very heavily on computer science algorithms as research tools. The process of finding the longest common subsequence of two DNA sequences has a wide range of applications in modern bioinformatics. Genetics databases can hold enormous amounts of raw data, for example the human genome consists of approximately three billion DNA base pairs. The processing of this gigantic volume of data necessitates the use of extremely efficient string algorithms. This paper introduces a space and time effective technique for retrieving the longest common subsequence of DNA sequences.

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Konsavage, Wesley M., Stephen Burkholder, Malgorzata Sudol, Amy L. Harper, and Michael Katzman. "A Substitution in Rous Sarcoma Virus Integrase That Separates Its Two Biologically Relevant Enzymatic Activities." Journal of Virology 79, no. 8 (April 15, 2005): 4691–99. http://dx.doi.org/10.1128/jvi.79.8.4691-4699.2005.

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ABSTRACT Retroviral integrase prepares viral DNA for integration by removing 2 nucleotides from each end of unintegrated DNA in a reaction referred to as processing. However, it has been known since the processing assay was first described that avian integrases frequently nick 3 nucleotides, as well as 2 nucleotides, from viral DNA ends when reaction mixtures contain Mn2+. We now report that specificity for the biologically relevant “−2” site is enhanced when the serine at amino acid 124 of Rous sarcoma virus (RSV) integrase is replaced by alanine, valine, glycine, lysine, or aspartate. The protein with a serine-to-aspartate substitution exhibited especially high fidelity for the correct site, as evidenced by a ratio of −2 nicks to −3 nicks that was more than 40-fold greater than that for the wild-type enzyme in reactions with Mn2+. Even with Mg2+, the substituted proteins exhibited greater specificity than the wild type, especially the S124D protein. Moreover, this protein was more efficient than the wild type at processing viral DNA ends. Unexpectedly, however, the S124D protein was significantly impaired at catalyzing the insertion of viral DNA ends in reactions with Mn2+ and joining was undetectable in reactions with Mg2+. Thus, the S124D protein has separated the processing and joining activities of integrase. Similar results were found for human immunodeficiency virus integrase with the analogous substitution. No proteins with comparable properties have been described. Moreover, RSV virions containing integrase with the S124D mutation were unable to replicate in cell cultures. Together, these data suggest that integrase has evolved to have submaximal processing activity so that it can also catalyze DNA joining.

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Hrabina, Ondrej, Viktor Brabec, and Olga Novakova. "Translesion DNA Synthesis Across Lesions Induced by Oxidative Products of Pyrimidines: An Insight into the Mechanism by Microscale Thermophoresis." International Journal of Molecular Sciences 20, no. 20 (October 10, 2019): 5012. http://dx.doi.org/10.3390/ijms20205012.

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Oxidative stress in cells can lead to the accumulation of reactive oxygen species and oxidation of DNA precursors. Oxidized nucleotides such as 2’-deoxyribo-5-hydroxyuridin (HdU) and 2’-deoxyribo-5-hydroxymethyluridin (HMdU) can be inserted into DNA during replication and repair. HdU and HMdU have attracted particular interest because they have different effects on damaged-DNA processing enzymes that control the downstream effects of the lesions. Herein, we studied the chemically simulated translesion DNA synthesis (TLS) across the lesions formed by HdU or HMdU using microscale thermophoresis (MST). The thermodynamic changes associated with replication across HdU or HMdU show that the HdU paired with the mismatched deoxyribonucleoside triphosphates disturbs DNA duplexes considerably less than thymidine (dT) or HMdU. Moreover, we also demonstrate that TLS by DNA polymerases across the lesion derived from HdU was markedly less extensive and potentially more mutagenic than that across the lesion formed by HMdU. Thus, DNA polymerization by DNA polymerase η (polη), the exonuclease-deficient Klenow fragment of DNA polymerase I (KF–), and reverse transcriptase from human immunodeficiency virus type 1 (HIV-1 RT) across these pyrimidine lesions correlated with the different stabilization effects of the HdU and HMdU in DNA duplexes revealed by MST. The equilibrium thermodynamic data obtained by MST can explain the influence of the thermodynamic alterations on the ability of DNA polymerases to bypass lesions induced by oxidative products of pyrimidines. The results also highlighted the usefulness of MST in evaluating the impact of oxidative products of pyrimidines on the processing of these lesions by damaged DNA processing enzymes.

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Maass, Kendra K., Paulina S. Schad, Agnes M. E. Finster, Pitithat Puranachot, Fabian Rosing, Tatjana Wedig, Nathalie Schwarz, Natalie Stumpf, Stefan M. Pfister, and Kristian W. Pajtler. "From Sampling to Sequencing: A Liquid Biopsy Pre-Analytic Workflow to Maximize Multi-Layer Genomic Information from a Single Tube." Cancers 13, no. 12 (June 15, 2021): 3002. http://dx.doi.org/10.3390/cancers13123002.

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Liquid biopsies hold great promise for the management of cancer. Reliable liquid biopsy data depend on stable and reproducible pre-analytical protocols that comply with quality measures, irrespective of the sampling and processing site. We established a workflow for plasma preservation, followed by processing, cell-free nucleic acid isolation, quantification, and enrichment of potentially tumor-derived cell-free DNA and RNA. Employing the same input material for a direct comparison of different kits and protocols allowed us to formulate unbiased recommendations for sample collection, storage, and processing. The presented workflow integrates the stabilization in Norgen, PAX, or Streck tubes and subsequent parallel isolation of cell-free DNA and RNA with NucleoSnap and NucleoSpin. Qubit, Bioanalyzer, and TapeStation quantification and quality control steps were optimized for minimal sample use and high sensitivity and reproducibility. We show the efficiency of the proposed workflow by successful droplet digital PCR amplification of both cell-free DNA and RNA and by detection of tumor-specific alterations in low-coverage whole-genome sequencing and DNA methylation profiling of plasma-derived cell-free DNA. For the first time, we demonstrated successful parallel extraction of cell-free DNA and RNA from plasma samples. This workflow paves the road towards multi-layer genomic analysis from one single liquid biopsy sample.

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Zisis, Dimitrios, Paweł Krajewski, Maike Stam, Blaise Weber, and Iris Hövel. "Analysis of 4C-seq data: A comparison of methods." Journal of Bioinformatics and Computational Biology 18, no. 01 (February 2020): 2050001. http://dx.doi.org/10.1142/s0219720020500018.

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The circular chromosome conformation capture technique followed by sequencing (4C-seq) has been used in a number of studies to investigate chromosomal interactions between DNA fragments. Computational pipelines have been developed and published that offer various possibilities of 4C-seq data processing and statistical analysis. Here, we present an overview of four of such pipelines (fourSig, FourCSeq, 4C-ker and w4Cseq) taking into account the most important stages of computations. We provide comparisons of the methods and discuss their advantages and possible weaknesses. We illustrate the results with the use of data obtained for two different species, in a study devoted to vernalization control in Arabidopsis thaliana by the FLOWERING LOCUS C (FLC) gene and to long-range chromatin interactions in mouse embryonic stem cells.

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Journal articles on the topic 'DNA - Data processing'

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