Relevant bibliographies by topics / Genomic search

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Genomic search'

Author: Grafiati
Published: 4 June 2021
Last updated: 1 February 2022

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Journal articles on the topic "Genomic search"

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Montanari, Piero, Ilaria Bartolini, Paolo Ciaccia, Marco Patella, Stefano Ceri, and Marco Masseroli. "Pattern Similarity Search in Genomic Sequences." IEEE Transactions on Knowledge and Data Engineering 28, no. 11 (November 1, 2016): 3053–67. http://dx.doi.org/10.1109/tkde.2016.2595582.

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Wei-Mou, Zheng. "Genomic Signal Search by Dynamic Programming." Communications in Theoretical Physics 39, no. 6 (June 15, 2003): 761–64. http://dx.doi.org/10.1088/0253-6102/39/6/761.

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Fernandez, Javier D., Maurizio Lenzerini, Marco Masseroli, Francesco Venco, and Stefano Ceri. "Ontology-Based Search of Genomic Metadata." IEEE/ACM Transactions on Computational Biology and Bioinformatics 13, no. 2 (March 1, 2016): 233–47. http://dx.doi.org/10.1109/tcbb.2015.2495179.

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Howe, Kevin L., Premanand Achuthan, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M. Ridwan Amode, Irina M. Armean, et al. "Ensembl 2021." Nucleic Acids Research 49, no. D1 (November 2, 2020): D884—D891. http://dx.doi.org/10.1093/nar/gkaa942.

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Abstract The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our integrated genomic data are made available in a variety of ways, including genome browsers, search interfaces, specialist tools such as the Ensembl Variant Effect Predictor, download files and programmatic interfaces. Here, we present recent Ensembl developments including two new website portals. Ensembl Rapid Release (http://rapid.ensembl.org) is designed to provide core tools and services for genomes as soon as possible and has been deployed to support large biodiversity sequencing projects. Our SARS-CoV-2 genome browser (https://covid-19.ensembl.org) integrates our own annotation with publicly available genomic data from numerous sources to facilitate the use of genomics in the international scientific response to the COVID-19 pandemic. We also report on other updates to our annotation resources, tools and services. All Ensembl data and software are freely available without restriction.
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Cannon, Ethalinda K. S., Scott M. Birkett, Bremen L. Braun, Sateesh Kodavali, Douglas M. Jennewein, Alper Yilmaz, Valentin Antonescu, et al. "POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data." International Journal of Plant Genomics 2011 (December 27, 2011): 1–10. http://dx.doi.org/10.1155/2011/923035.

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The purpose of the online resource presented here, POPcorn (Project Portal for corn), is to enhance accessibility of maize genetic and genomic resources for plant biologists. Currently, many online locations are difficult to find, some are best searched independently, and individual project websites often degrade over time—sometimes disappearing entirely. The POPcorn site makes available (1) a centralized, web-accessible resource to search and browse descriptions of ongoing maize genomics projects, (2) a single, stand-alone tool that uses web Services and minimal data warehousing to search for sequence matches in online resources of diverse offsite projects, and (3) a set of tools that enables researchers to migrate their data to the long-term model organism database for maize genetic and genomic information: MaizeGDB. Examples demonstrating POPcorn’s utility are provided herein.
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Garczarek, Laurence, Ulysse Guyet, Hugo Doré, Gregory K. Farrant, Mark Hoebeke, Loraine Brillet-Guéguen, Antoine Bisch, et al. "Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes." Nucleic Acids Research 49, no. D1 (October 30, 2020): D667—D676. http://dx.doi.org/10.1093/nar/gkaa958.

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Abstract Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites. The main entry to the database is through search for a term (gene name, product, etc.), resulting in a list of CLOGs and individual genes. Each CLOG benefits from a rich functional annotation including EggNOG, EC/K numbers, GO terms, TIGR Roles, custom-designed Cyanorak Roles as well as several protein motif predictions. Cyanorak also displays a phyletic profile, indicating the genotype and pigment type for each CLOG, and a genome viewer (Jbrowse) to visualize additional data on each genome such as predicted operons, genomic islands or transcriptomic data, when available. This information system also includes a BLAST search tool, comparative genomic context as well as various data export options. Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms.
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Dutton, Gail. "CRISPR Retooled as a Genomic Search Engine." Genetic Engineering & Biotechnology News 38, no. 20 (November 15, 2018): 6–7. http://dx.doi.org/10.1089/gen.38.20.05.

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Wilson, Tyler J., and Steven X. Ge. "ArraySearch: A Web-Based Genomic Search Engine." Comparative and Functional Genomics 2012 (2012): 1–10. http://dx.doi.org/10.1155/2012/650842.

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Recent advances in microarray technologies have resulted in a flood of genomics data. This large body of accumulated data could be used as a knowledge base to help researchers interpret new experimental data. ArraySearch finds statistical correlations between newly observed gene expression profiles and the huge source of well-characterized expression signatures deposited in the public domain. A search query of a list of genes will return experiments on which the genes are significantly up- or downregulated collectively. Searches can also be conducted using gene expression signatures from new experiments. This resource will empower biological researchers with a statistical method to explore expression data from their own research by comparing it with expression signatures from a large public archive.
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Chan, Sarah. "In search of a post-genomic bioethics." History of the Human Sciences 31, no. 1 (February 2018): 116–23. http://dx.doi.org/10.1177/0952695117729119c.

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Kopanos, Christos, Vasilis Tsiolkas, Alexandros Kouris, Charles E. Chapple, Monica Albarca Aguilera, Richard Meyer, and Andreas Massouras. "VarSome: the human genomic variant search engine." Bioinformatics 35, no. 11 (October 30, 2018): 1978–80. http://dx.doi.org/10.1093/bioinformatics/bty897.

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Dissertations / Theses on the topic "Genomic search"

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Cameron, Michael, and mcam@mc-mc net. "Efficient Homology Search for Genomic Sequence Databases." RMIT University. Computer Science and Information Technology, 2006. http://adt.lib.rmit.edu.au/adt/public/adt-VIT20070509.162443.

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Genomic search tools can provide valuable insights into the chemical structure, evolutionary origin and biochemical function of genetic material. A homology search algorithm compares a protein or nucleotide query sequence to each entry in a large sequence database and reports alignments with highly similar sequences. The exponential growth of public data banks such as GenBank has necessitated the development of fast, heuristic approaches to homology search. The versatile and popular blast algorithm, developed by researchers at the US National Center for Biotechnology Information (NCBI), uses a four-stage heuristic approach to efficiently search large collections for analogous sequences while retaining a high degree of accuracy. Despite an abundance of alternative approaches to homology search, blast remains the only method to offer fast, sensitive search of large genomic collections on modern desktop hardware. As a result, the tool has found widespread use with millions of queries posed each day. A significant investment of computing resources is required to process this large volume of genomic searches and a cluster of over 200 workstations is employed by the NCBI to handle queries posed through the organisation's website. As the growth of sequence databases continues to outpace improvements in modern hardware, blast searches are becoming slower each year and novel, faster methods for sequence comparison are required. In this thesis we propose new techniques for fast yet accurate homology search that result in significantly faster blast searches. First, we describe improvements to the final, gapped alignment stages where the query and sequences from the collection are aligned to provide a fine-grain measure of similarity. We describe three new methods for aligning sequences that roughly halve the time required to perform this computationally expensive stage. Next, we investigate improvements to the first stage of search, where short regions of similarity between a pair of sequences are identified. We propose a novel deterministic finite automaton data structure that is significantly smaller than the codeword lookup table employed by ncbi-blast, resulting in improved cache performance and faster search times. We also discuss fast methods for nucleotide sequence comparison. We describe novel approaches for processing sequences that are compressed using the byte packed format already utilised by blast, where four nucleotide bases from a strand of DNA are stored in a single byte. Rather than decompress sequences to perform pairwise comparisons, our innovations permit sequences to be processed in their compressed form, four bases at a time. Our techniques roughly halve average query evaluation times for nucleotide searches with no effect on the sensitivity of blast. Finally, we present a new scheme for managing the high degree of redundancy that is prevalent in genomic collections. Near-duplicate entries in sequence data banks are highly detrimental to retrieval performance, however existing methods for managing redundancy are both slow, requiring almost ten hours to process the GenBank database, and crude, because they simply purge highly-similar sequences to reduce the level of internal redundancy. We describe a new approach for identifying near-duplicate entries that is roughly six times faster than the most successful existing approaches, and a novel approach to managing redundancy that reduces collection size and search times but still provides accurate and comprehensive search results. Our improvements to blast have been integrated into our own version of the tool. We find that our innovations more than halve average search times for nucleotide and protein searches, and have no signifcant effect on search accuracy. Given the enormous popularity of blast, this represents a very significant advance in computational methods to aid life science research.
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Smargon, Aaron Andrew. "An expanded search for RNA-programmable genomic engineering effectors." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/105959.

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Thesis: S.M., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2016.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 31-33).
A biocomputational pipeline was designed and implemented to mine through metagenomic datasets for novel Class 2 CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) single effectors, akin to the revolutionary genome-engineering tools Cas9 and Cpf1. Whereas previous search strategies relied on protein proximity to CRISPR-associated spacer acquisition proteins Cas1 and Cas2, this approach was seeded on CRISPR arrays alone. What resulted was the discovery of a potential new Class 2 CRISPR system, with two subtypes as characterized by distinct putative accessory proteins. Follow-up experimental work is required to assess the system's activity: first, in the presence and absence of the accessory protein; and second, as a single effector protein capable of precise genome engineering in prokaryotic and eukaryotic cells.
by Aaron Andrew Smargon.
S.M.
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Sheren, Jamie Elizabeth. "Identifying functional lox sequences: A genomic search and randomized libraries." Connect to online resource, 2007. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3273689.

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Lindblad, Kerstin. "Genomic studies of expanded trinucleotide repeats : focus on neuropsychiatric disorders /." Stockholm, 1998. http://diss.kib.ki.se/search/diss.se.cfm?19980904lind.

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Skutas, Jorie L. "Microbial and Genomic Analysis of Environmental Samples in Search of Pathogenic Salmonella." NSUWorks, 2017. http://nsuworks.nova.edu/occ_stuetd/461.

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Salmonellosis or “food poisoning” is a foodborne infection brought on by the pathogen Salmonella from the ingestion of the bacterium on contaminated foods such as vegetables. Infection from Salmonella leads to the highest incidence of hospitalizations and deaths each year, compared to any other bacterial foodborne illness. South Florida is the second largest agricultural winter vegetable producer in the United States, and contamination of vegetables is often observed in preharvest practices. A hardy bacterium, Salmonella, has been shown to live up to 6 weeks in soil and water up to 42°C without a host. The Florida Everglades is a tropical wetland that plays a large role in South Florida’s watershed. It can be divided into agricultural, conservation, and urban areas that connect Lake Okeechobee to Florida Bay by canals, swamps, and rivers. Inland canals tightly regulate water levels in South Florida as a means of flood control for residential and agricultural land. With the influences of anthropomorphic run off from agricultural and urban use, we hypothesized that microbial communities would significantly differ between three select sites in western (Collier county) versus three sites in more urban eastern Florida (Broward county): natural standing water, manmade drainage canal in agricultural areas, and manmade drainage canals in urban areas. We also hypothesized that pathogenic like Salmonella would be present in these habitats. Deep sequencing and ecological genetics analyses of the 16s rRNA V4 region yielded a total of 163,320 unique bacterial OTUs from a total of 139 samples collected monthly for one year in 2015 and part of 2016. Salmonella is not considered an abundant taxon within the microbial population. With the knowledge that Salmonella resides within the microbial population isolates were cultured from soil and water samples that were taken monthly from each site using a modified version of the Food and Drug Administration Bacterial Analytical Methods manual (FDA-BAM). The culturing resulted in 234 isolates obtained and 31 different serovars of Salmonella. Culturing showed that Salmonella favored months with high standing water and high-water temperatures that would lead to the ideal environment for survival. The most commonly occurring isolates within the sample set are those associated with agricultural animals. Though Salmonella may be a rare taxon within the microbial population given the correct environmental conditions such as warm temperatures it is possible to observe Salmonella year round within the South Florida environment.
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Sigdel, Tara. "A Search for Zn(II) Metallochaperones in E. coli, Proteomic and Genomic Approaches." Miami University / OhioLINK, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=miami1128394584.

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Rooney, Patrick Hugh. "A genomic approach to the study of chemoresistance." Thesis, University of Aberdeen, 2000. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU602009.

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This study evaluated comparative genomic hybridisation (CGH) as a tool to detect candidate regions of the genome associated with chemoresistance. Using a variation on conventional CGH, DNA from three cell lines that were resistant to thymidylate synthase (TS) inhibitors (tomudex [TDX] or 5-fluorouracil [5-FU]) and their sensitive parent cells were evaluated. In MCF-7 and H630, cells that were resistant to TDX, a specific TS inhibitor with no other known cytotoxic potential, only a single region of change (18p gain) was apparent. The third cell line H630R10, which was resistant to 5-FU, had changes in several genomic regions following the acquisition of resistance, including 18p. Gain in the chromosomal region containing the TS gene (18pll.32) was detected by CGH in all three resistant cell lines. However, additional novel regions of interest were identified in the cells that were resistant to 5-FU, a cytotoxic agent known to have several other modes of cytotoxicity besides TS inhibition. These results suggested that CGH is of potential use in the detection of regions of the genome involved in chemoresistance. Having shown the potential of CGH as a tool for assessing chemoresistance at the genomic level, steps toward clinical application of this technique were evaluated. A prerequisite for study in archival pathology samples was successful DNA extraction and universal amplification of tumour DNA from paraffin-embedded tumour sections for CGH analysis. Degenerate oligonucleotide primed - polymerase chain reaction (DOP-PCR) was performed on minute quantities (50ngs) of fresh cell line DNA (H630R10) and tumour DNA (osteosarcoma), as well as paraffin-embedded DNA from the same case. The results of these DOP-PCR CGH reactions were compared with conventional CGH using l|0.g quantities of fresh DNA from both H630R10 cell line and osteosarcoma. The CGH profiles of the conventional CGH and DOP-PCR CGH did not show a high level of concordance, only 55% of the gains and 83.3% of losses detected by conventional CGH were detected by DOP-PCR CGH The use of universal amplification by DOP-PCR in paraffin-embedded sections was not taken forward into clinical evaluation. A study of colorectal cancer (CRC) was initiated which involved the microdissection of 29 Dukes' C CRC tumours from fresh frozen material for CGH analysis. This conventional CGH analysis of CRC tumours involved assessing each tumour twice by reversal of fluorochromes. Only genomic regions that were detected as changed in both forward and reverse profiles were accepted. This approach detected several regions of genome as changed across the 29 tumours. In all, 108 gains (a mean number of 3.7 aberrations per tumour, range 1-12) and 85 losses (a mean number of 2.9 aberrations per tumour, range 0-11) were detected in the 29 tumours. CGH analyses identified certain chromosomal regions as more likely to be changed than others. The most frequent aberrations detected across the 29 tumours was a loss of chromosomal arm 18q, seen in 31% of the tumours assessed. Gain was also common at some sites throughout the genome, for example, gain of chromosomal arms, 13q and 20q was seen in 27.6% of cases. Mann-Whitney U tests investigating the association between specific chromosomal aberrations such as gain of 20q or loss of 18q and known markers of CRC tumourigenesis (p53, p27, p21, Rb, cyclin Dl, PCNA, P-catenin, e-cadherin, c-erbB-2, bcl2, EGFR and c-erbB-2) assessed by immunohistochemistry (IHC) in 29 tumours found no association. Testing of the total number of genomic aberrations detected (loss + gain = genetic grade) rather than the frequency of aberration at specific chromosomal loci also found no association with the CRC tumour markers. Finally, the association between the chromosomal aberrations detected by CGH was investigated in relation to patient survival. This thesis has demonstrated the value of a global approach to the study of chemoresistance and tumourigenesis through the application of powerful technology such as CGH.
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Berrutti, Paula Dandara da Silva. "Genomic search of transposable elementsand their implications for the variability of pest species of fruit culture." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2018. http://hdl.handle.net/10183/187236.

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Burkhart, Tandace L. "The Search for Novel Sponge genes: Comparative Analysis of Gene Expression in Multiple Sponges." NSUWorks, 2012. http://nsuworks.nova.edu/occ_stuetd/194.

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This project focuses on the use of sponge genetic transcripts in the form of expressed sequence tags (ESTs) readily available in Genbank to search for novel genes using bioinformatics analysis tools. Marine sponge species are known to house a diversity of marine microbes and are known as the ‘living fossils’ of the animal kingdom because of the large number of ancient genes they house. Genomic mining can be a useful tool in discovering these orthologous genes. This study utilized the techniques of genomic mining of 11 previously described sponge species transcripts. The results of this study provide a better understanding of the genomic structure of the organisms studied by creating a more detailed genetic map and examining a specific environmental snapshot of the genes in each sponge. Novel methods for dissecting beneficial information from large scale data sets available in genomic libraries utilizing bioinformatics search tool MGRAST were examined. The results of this study indicate that sponges house numerous genes that are likely to be evolutionary predecessors of genes in higher eukaryotes. Support was also given to the notion that microbial communities play a role in metabolic pathways of sponges.
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Sun, Wenhai. "Towards Secure Outsourced Data Services in the Public Cloud." Diss., Virginia Tech, 2018. http://hdl.handle.net/10919/84396.

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Past few years have witnessed a dramatic shift for IT infrastructures from a self-sustained model to a centralized and multi-tenant elastic computing paradigm -- Cloud Computing, which significantly reshapes the landscape of existing data utilization services. In truth, public cloud service providers (CSPs), e.g. Google, Amazon, offer us unprecedented benefits, such as ubiquitous and flexible access, considerable capital expenditure savings and on-demand resource allocation. Cloud has become the virtual ``brain" as well to support and propel many important applications and system designs, for example, artificial intelligence, Internet of Things, and so forth; on the flip side, security and privacy are among the primary concerns with the adoption of cloud-based data services in that the user loses control of her/his outsourced data. Encrypting the sensitive user information certainly ensures the confidentiality. However, encryption places an extra layer of ambiguity and its direct use may be at odds with the practical requirements and defeat the purpose of cloud computing technology. We believe that security in nature should not be in contravention of the cloud outsourcing model. Rather, it is expected to complement the current achievements to further fuel the wide adoption of the public cloud service. This, in turn, requires us not to decouple them from the very beginning of the system design. Drawing the successes and failures from both academia and industry, we attempt to answer the challenges of realizing efficient and useful secure data services in the public cloud. In particular, we pay attention to security and privacy in two essential functions of the cloud ``brain", i.e. data storage and processing. Our first work centers on the secure chunk-based deduplication of encrypted data for cloud backup and achieves the performance comparable to the plaintext cloud storage deduplication while effectively mitigating the information leakage from the low-entropy chunks. On the other hand, we comprehensively study the promising yet challenging issue of search over encrypted data in the cloud environment, which allows a user to delegate her/his search task to a CSP server that hosts a collection of encrypted files while still guaranteeing some measure of query privacy. In order to accomplish this grand vision, we explore both software-based secure computation research that often relies on cryptography and concentrates on algorithmic design and theoretical proof, and trusted execution solutions that depend on hardware-based isolation and trusted computing. Hopefully, through the lens of our efforts, insights could be furnished into future research in the related areas.
Ph. D.
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Books on the topic "Genomic search"

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Ahmed, Tariq. Search for RAS-like genes in the C.albicans genome. Manchester: UMIST, 1995.

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Dr. B.P. Pal Birth Centenary Symposium (2006 National Academy of Agricultural Sciences). Search for new genes. Edited by Pal B. P. 1906-1989, Chopra V. L, and National Academy of Agricultural Sciences. New Delhi: Academic Foundation in association with National Academy of Agricultural Sciences, 2007.

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Dr. B.P. Pal Birth Centenary Symposium (2006 National Academy of Agricultural Sciences). Search for new genes. Edited by Chopra V. L, Pal B. P. 1906-1989, and National Academy of Agricultural Sciences. New Delhi: Academic Foundation in association with National Academy of Agricultural Sciences, 2007.

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Tanzi, Rudolph E. Decoding darkness: The search for the genetic causes of Alzheimer's disease. Cambridge, Mass: Perseus Publishing, 2000.

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Tanzi, Rudolph E. Decoding darkness: The search for the genetic causes of Alzheimer's disease. Cambridge, Mass: Perseus Pub., 2000.

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B, Parson Ann, ed. Decoding darkness: The search for the genetic causes of Alzheimer's disease. Cambridge, Mass: Perseus Publ., 2000.

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Neanderthal Man In Search Of Lost Genomes. Basic Books, 2013.

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Pääbo, Svante. Neanderthal Man: In Search of Lost Genomes. 2016.

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Walsh, Bruce, and Michael Lynch. Using Molecular Data to Detect Selection: Signatures from Multiple Historical Events. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198830870.003.0010.

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This chapter examines the search for a pattern of repetitive adaptive substitutions over evolutionary time. In contrast with the previous chapter, only a modest number of tests toward this aim have been proposed. The HKA and McDonald-Kreitman tests contrast the polymorphism to divergence ratio between different genomic classes (such as different genes or silent versus replacement sites within the same gene). These approaches can detect an excess of substitutions, which allows one to estimate the fraction of adaptive sites. This chapter reviews the empirical data on estimates of this fraction and discusses some of the sources of bias it its estimation. Over an even longer time scale, one can contrast the rate of change of sites in a sequence over a phylogeny. These tests require a rather special type of selection, wherein the same specific site (usually a codon) experiences multiple adaptive substitutions over a phylogeny, such as might occur in arms-race genes.
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(Editor), V. L. Chopra, R. P. Sharma (Editor), S. R. Bhat (Editor), and B. M. Prasanna (Editor), eds. Search for New Genes. Academic Foundation, 2007.

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Book chapters on the topic "Genomic search"

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Dorronsoro, Bernabé, Pascal Bouvry, and Enrique Alba. "Iterated Local Search for de Novo Genomic Sequencing." In Artifical Intelligence and Soft Computing, 428–36. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-13232-2_52.

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Lenne, Renaud, Christine Solnon, Thomas Stützle, Eric Tannier, and Mauro Birattari. "Reactive Stochastic Local Search Algorithms for the Genomic Median Problem." In Evolutionary Computation in Combinatorial Optimization, 266–76. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-78604-7_23.

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Carretero-Paulet, Lorenzo, and Victor A. Albert. "Sequence Search and Comparative Genomic Analysis of SUMO-Activating Enzymes Using CoGe." In Methods in Molecular Biology, 261–72. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3759-2_21.

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Rheinländer, Astrid, Martin Knobloch, Nicky Hochmuth, and Ulf Leser. "Prefix Tree Indexing for Similarity Search and Similarity Joins on Genomic Data." In Lecture Notes in Computer Science, 519–36. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-13818-8_36.

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Gräf, Stefan, Jan-Hendrik Teune, Dirk Strothmann, Stefan Kurtz, and Gerhard Steger. "A Computational Approach to Search for Non-Coding RNAs in Large Genomic Data." In Small RNAs, 57–74. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/978-3-540-28130-6_3.

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Parker, Stephen C. J., Aaron Harlap, and Thomas D. Tullius. "A Computational Method to Search for DNA Structural Motifs in Functional Genomic Elements." In Methods in Molecular Biology, 367–79. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-173-4_21.

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Saitou, Naruya. "Homology Search and Multiple Alignment." In Introduction to Evolutionary Genomics, 325–60. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-92642-1_15.

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Buhler, Jeremy, and Rachel Nordgren. "Toward a Phylogenetically Aware Algorithm for Fast DNA Similarity Search." In Comparative Genomics, 15–29. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/978-3-540-32290-0_2.

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Ojopi, Elida P. B., Sheila Passos Gregorio, Pedro Edson Moreira Guimarães, Cintia Fridman, and Emmanuel Dias Neto. "Human genome and the perspectives for schizophrenia." In Search for the Causes of Schizophrenia, 278–96. Heidelberg: Steinkopff, 2004. http://dx.doi.org/10.1007/978-3-7985-1953-4_19.

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Davot, Tom, Annie Chateau, Rodolphe Giroudeau, and Mathias Weller. "Linearizing Genomes: Exact Methods and Local Search." In SOFSEM 2020: Theory and Practice of Computer Science, 505–18. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-38919-2_41.

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Conference papers on the topic "Genomic search"

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Nałęcz-Charkiewicz, Katarzyna, and Robert Nowak. "Algorithm to search for genomic rearrangements." In Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2013, edited by Ryszard S. Romaniuk. SPIE, 2013. http://dx.doi.org/10.1117/12.2032639.

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Pandey, S., M. D. Kane, and J. A. Springer. "GLASS: Genomic Literature Area Sequence Search." In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW). IEEE, 2011. http://dx.doi.org/10.1109/bibmw.2011.6112436.

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"GAST, A GENOMIC ALIGNMENT SEARCH TOOL." In International Conference on Bioinformatics Models, Methods and Algorithms. SciTePress - Science and and Technology Publications, 2011. http://dx.doi.org/10.5220/0003181400820090.

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Xiaochun Yang, Bin Wang, Chen Li, Jiaying Wang, and Xiaohui Xie. "Efficient direct search on compressed genomic data." In 2013 29th IEEE International Conference on Data Engineering (ICDE 2013). IEEE, 2013. http://dx.doi.org/10.1109/icde.2013.6544889.

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Zhang, Wangda, Mengdi Lin, and Kenneth A. Ross. "Efficient Search over Genomic Short Read Data." In SSDBM 2020: 32nd International Conference on Scientific and Statistical Database Management. New York, NY, USA: ACM, 2020. http://dx.doi.org/10.1145/3400903.3400907.

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Mahdi, Md Safiur Rahman, Mohammad Zahidul Hasan, and Noman Mohammed. "Secure Sequence Similarity Search on Encrypted Genomic Data." In 2017 IEEE/ACM International Conference on Connected Health: Applications, Systems and Engineering Technologies (CHASE). IEEE, 2017. http://dx.doi.org/10.1109/chase.2017.79.

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Bradshaw, Jordan A., Rasha Karakchi, and Jason D. Bakos. "Two-Hit Filter Synthesis for Genomic Database Search." In 2016 IEEE 24th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM). IEEE, 2016. http://dx.doi.org/10.1109/fccm.2016.24.

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Buhler, Jeremy, Uri Keich, and Yanni Sun. "Designing seeds for similarity search in genomic DNA." In the seventh annual international conference. New York, New York, USA: ACM Press, 2003. http://dx.doi.org/10.1145/640075.640083.

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Wang, Yuanrong, Xueqi Li, Dawei Zang, Guangming Tan, and Ninghui Sun. "Accelerating FM-index Search for Genomic Data Processing." In ICPP 2018: 47th International Conference on Parallel Processing. New York, NY, USA: ACM, 2018. http://dx.doi.org/10.1145/3225058.3225134.

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Sacan, Ahmet, and I. Hakki Toroslu. "Approximate Similarity Search in Genomic Sequence Databases Using Landmark-Guided Embedding." In 2008 First International Workshop on Similarity Search and Applications (SISAP). IEEE, 2008. http://dx.doi.org/10.1109/sisap.2008.7.

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Reports on the topic "Genomic search"

1

Li, Zhe, Douglas Linn, and Xin Zhang. Genome-wide Search of Oncogenic Pathways Cooperating with ETS Fusions in Prostate Cancer. Fort Belvoir, VA: Defense Technical Information Center, July 2013. http://dx.doi.org/10.21236/ada586039.

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