Relevant bibliographies by topics / Genome reconstruction

Contents

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

Academic literature on the topic 'Genome reconstruction'

Author: Grafiati
Published: 4 June 2021
Last updated: 15 June 2025

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Journal articles on the topic "Genome reconstruction"

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Avdeyev, Pavel, Nikita Alexeev, Yongwu Rong, and Max A. Alekseyev. "A unified ILP framework for core ancestral genome reconstruction problems." Bioinformatics 36, no. 10 (2020): 2993–3003. http://dx.doi.org/10.1093/bioinformatics/btaa100.

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Abstract Motivation One of the key computational problems in comparative genomics is the reconstruction of genomes of ancestral species based on genomes of extant species. Since most dramatic changes in genomic architectures are caused by genome rearrangements, this problem is often posed as minimization of the number of genome rearrangements between extant and ancestral genomes. The basic case of three given genomes is known as the genome median problem. Whole-genome duplications (WGDs) represent yet another type of dramatic evolutionary events and inspire the reconstruction of preduplicated
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Nelson, William C., Benjamin J. Tully, and Jennifer M. Mobberley. "Biases in genome reconstruction from metagenomic data." PeerJ 8 (October 30, 2020): e10119. http://dx.doi.org/10.7717/peerj.10119.

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Background Advances in sequencing, assembly, and assortment of contigs into species-specific bins has enabled the reconstruction of genomes from metagenomic data (MAGs). Though a powerful technique, it is difficult to determine whether assembly and binning techniques are accurate when applied to environmental metagenomes due to a lack of complete reference genome sequences against which to check the resulting MAGs. Methods We compared MAGs derived from an enrichment culture containing ~20 organisms to complete genome sequences of 10 organisms isolated from the enrichment culture. Factors commo
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Drillon, Guénola, Raphaël Champeimont, Francesco Oteri, Gilles Fischer, and Alessandra Carbone. "Phylogenetic Reconstruction Based on Synteny Block and Gene Adjacencies." Molecular Biology and Evolution 37, no. 9 (2020): 2747–62. http://dx.doi.org/10.1093/molbev/msaa114.

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Abstract Gene order can be used as an informative character to reconstruct phylogenetic relationships between species independently from the local information present in gene/protein sequences. PhyChro is a reconstruction method based on chromosomal rearrangements, applicable to a wide range of eukaryotic genomes with different gene contents and levels of synteny conservation. For each synteny breakpoint issued from pairwise genome comparisons, the algorithm defines two disjoint sets of genomes, named partial splits, respectively, supporting the two block adjacencies defining the breakpoint. C
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Zorrilla, Francisco, Filip Buric, Kiran R. Patil, and Aleksej Zelezniak. "metaGEM: reconstruction of genome scale metabolic models directly from metagenomes." Nucleic Acids Research 49, no. 21 (2021): e126-e126. http://dx.doi.org/10.1093/nar/gkab815.

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Abstract Metagenomic analyses of microbial communities have revealed a large degree of interspecies and intraspecies genetic diversity through the reconstruction of metagenome assembled genomes (MAGs). Yet, metabolic modeling efforts mainly rely on reference genomes as the starting point for reconstruction and simulation of genome scale metabolic models (GEMs), neglecting the immense intra- and inter-species diversity present in microbial communities. Here, we present metaGEM (https://github.com/franciscozorrilla/metaGEM), an end-to-end pipeline enabling metabolic modeling of multi-species com
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AHREN, DAG G., and CHRISTOS A. OUZOUNIS. "ROBUSTNESS OF METABOLIC MAP RECONSTRUCTION." Journal of Bioinformatics and Computational Biology 02, no. 03 (2004): 589–93. http://dx.doi.org/10.1142/s021972000400079x.

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With the ever increasing amount of genomic data available, the interest for generating biochemical pathways has grown tremendously. So far, mainly complete genomes have been used to reconstruct the biochemical pathways and their associated interactions. However, a large number of low coverage genomes, as well as other sources of partial genomic data, are currently available for many organisms. In order to be able to use incomplete data for metabolic reconstruction, the inherent properties of this procedure need to be investigated. In this short note, we describe the robustness and predictive p
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Boore, Jeffrey L., and Susan I. Fuerstenberg. "Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction." Philosophical Transactions of the Royal Society B: Biological Sciences 363, no. 1496 (2008): 1445–51. http://dx.doi.org/10.1098/rstb.2007.2234.

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The first whole genomes to be compared for phylogenetic inference were those of mitochondria, which provided the first sets of genome-level characters for phylogenetic reconstruction. Most powerful among these characters has been the comparisons of the relative arrangements of genes, which has convincingly resolved numerous branch points, including those that had remained recalcitrant even to very large molecular sequence comparisons. Now the world faces a tsunami of complete nuclear genome sequences. In addition to the tremendous amount of DNA sequence that is becoming available for compariso
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Seitz, Alexander, Friederike Hanssen, and Kay Nieselt. "DACCOR–Detection, characterization, and reconstruction of repetitive regions in bacterial genomes." PeerJ 6 (May 29, 2018): e4742. http://dx.doi.org/10.7717/peerj.4742.

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The reconstruction of genomes using mapping-based approaches with short reads experiences difficulties when resolving repetitive regions. These repetitive regions in genomes result in low mapping qualities of the respective reads, which in turn lead to many unresolved bases. Currently, the reconstruction of these regions is often based on modified references in which the repetitive regions are masked. However, for many references, such masked genomes are not available or are based on repetitive regions of other genomes. Our idea is to identify repetitive regions in the reference genome de novo
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Faria, José P., Miguel Rocha, Isabel Rocha, and Christopher S. Henry. "Methods for automated genome-scale metabolic model reconstruction." Biochemical Society Transactions 46, no. 4 (2018): 931–36. http://dx.doi.org/10.1042/bst20170246.

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In the era of next-generation sequencing and ubiquitous assembly and binning of metagenomes, new putative genome sequences are being produced from isolate and microbiome samples at ever-increasing rates. Genome-scale metabolic models have enormous utility for supporting the analysis and predictive characterization of these genomes based on sequence data. As a result, tools for rapid automated reconstruction of metabolic models are becoming critically important for supporting the analysis of new genome sequences. Many tools and algorithms have now emerged to support rapid model reconstruction a
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Zhang, Dezhi, Frank E. Rheindt, Huishang She, et al. "Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow." Systematic Biology 70, no. 5 (2021): 961–75. http://dx.doi.org/10.1093/sysbio/syab024.

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Abstract Phylogenetic trees based on genome-wide sequence data may not always represent the true evolutionary history for a variety of reasons. One process that can lead to incorrect reconstruction of species phylogenies is gene flow, especially if interspecific gene flow has affected large parts of the genome. We investigated phylogenetic relationships within a clade comprising eight species of passerine birds (Phylloscopidae, Phylloscopus, leaf warblers) using one de novo genome assembly and 78 resequenced genomes. On the basis of hypothesis-exclusion trials based on D-statistics, phylogenet
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Bochkareva, Olga O., Natalia O. Dranenko, Elena S. Ocheredko, et al. "Genome rearrangements and phylogeny reconstruction in Yersinia pestis." PeerJ 6 (March 27, 2018): e4545. http://dx.doi.org/10.7717/peerj.4545.

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Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleotide substitutions have occurred. On the other hand, even a small number of genome rearrangements may resolve topological ambiguities in a phylogenetic tree. We reconstructed phylogenetic trees based on genome rearrangements using several popular approaches such as Maximum likelihood for Gene Order a
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Dissertations / Theses on the topic "Genome reconstruction"

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Yang, Kuan. "Ancestral Genome Reconstruction in Bacteria." Diss., Virginia Tech, 2012. http://hdl.handle.net/10919/28091.

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The rapid accumulation of numerous sequenced genomes has provided a golden opportunity for ancestral state reconstruction studies, especially in the whole genome reconstruction area. However, most ancestral genome reconstruction methods developed so far only focus on gene or replicon sequences instead of whole genomes. They rely largely on either detailed modeling of evolutionary events or edit distance computation, both of which can be computationally prohibitive for large data sets. Hence, most of these methods can only be applied to a small number of features and species. In this dissertati
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Joseph, Sunitha. "Chromosome evolution and genome reconstruction in falcon species." Thesis, University of Kent, 2017. https://kar.kent.ac.uk/65667/.

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Falcons and falconry have become an essential part of life in the Middle East since ancient times. In the United Arab Emirates (UAE) itself, the number of trained falcons ranges from 8,000 to 10,000. Over the last five years, falcon racing, a traditional sport, has gained momentum in the UAE where captive falcons are competing for huge prizemoney. A proportion of the UAE economy goes into their care and conservation e.g. through establishing falcon hospitals with modern facilities for disease treatment and breeding as well as centers for diagnosis and research. Being the national bird of the U
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Penso, Dolfin Luca. "Genome reconstruction and combinatoric analyses of rearrangement evolution." Thesis, University of East Anglia, 2016. https://ueaeprints.uea.ac.uk/57181/.

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Cancer is often associated with a high number of large-scale, structural rearrangements. In a highly selective environment, some `driver' mutations conferring clonal growth advantage will be positively selected, accounting for further cancer development. Clarifying their nature, as well as their contribution to the pathology is a major current focus of biomedical research. Next generation sequencing technologies can be used nowadays to generate high-resolution data-sets of these alterations in cancer genomes. This project has been developed along two main lines: 1) the reconstruction of cancer
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Shanmugasundram, Achchuthan. "Genome annotation and metabolic reconstruction of apicomplexan parasites." Thesis, University of Liverpool, 2014. http://livrepository.liverpool.ac.uk/2004940/.

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The apicomplexans are causative agents of human and animal infections including malaria, toxoplasmosis and theileriosis and have a huge economic and social impact. A number of apicomplexan genomes have been sequenced. However, the annotation of gene functions remains challenging. A semi-automatic approach was used to systematically assign genes to their functions within pathways/networks through the integration of genomic information with biochemical evidence from the literature. This method has resulted in the evidence-based annotation of metabolic functions and the development of organism sp
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Hurlen, Natalie Christine. "Genome-scale reconstruction and analysis of eukaryotic metabolic networks." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2006. http://wwwlib.umi.com/cr/ucsd/fullcit?p3235012.

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Thesis (Ph. D.)--University of California, San Diego, 2006.<br>Title from first page of PDF file (viewed December 6, 2006). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 136-156).
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Loira, Nicolas. "Scaffold-based Reconstruction Method for Genome-Scale Metabolic Models." Phd thesis, Université Sciences et Technologies - Bordeaux I, 2012. http://tel.archives-ouvertes.fr/tel-00678991.

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La compréhension des organismes vivant a été une quête pendant longtemps. Depuis les premiers progrès des derniers siècles, nous sommes arrivés jusqu'au point où des quantités massives de données et d'information sont constamment générées. Bien que, jusqu'au present la plupart du travail a été concentré sur la génération d'un catalogue d'éléments biologiques, ce n'est pas que récemment qu'un effort coordonné pour dé- couvrir les réseaux de relations entre ces parties a'été constaté. Nous sommes intereses à comprendre non pas seulement ces réseaux, mais aussi la façon dont, à partir de ses conn
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Gautam, Jyotshana. "Genome-Scale Metabolic Network Reconstruction of Thermotoga sp.Strain RQ7." Bowling Green State University / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1605228158638208.

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Loira, Nicolas. "Scaffold-based reconstruction method of genome-scale metabolic models." Thesis, Bordeaux 1, 2012. http://www.theses.fr/2012BOR14484/document.

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La compréhension des organismes vivant a été une quête pendant longtemps. Depuisles premiers progrès des derniers siècles, nous sommes arrivés jusqu’au point où desquantités massives de données et d’information sont constamment générées. Bien que,jusqu’au présent la plupart du travail a été concentré sur la génération d’un catalogued’éléments biologiques, ce n’est pas que récemment qu’un effort coordonné pour découvrirles réseaux de relations entre ces parties a été constaté. Nous nous sommes intéressésà comprendre non pas seulement ces réseaux, mais aussi la façon dont, à partir de sesconnexi
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Tork, Bassam A. "VIRAL QUASISPECIES RECONSTRUCTION USING NEXT GENERATION SEQUENCING READS." Digital Archive @ GSU, 2013. http://digitalarchive.gsu.edu/cs_diss/77.

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The genomic diversity of viral quasispecies is a subject of great interest, especially for chronic infections. Characterization of viral diversity can be addressed by high-throughput sequencing technology (454 Life Sciences, Illumina, SOLiD, Ion Torrent, etc.). Standard assembly software was originally designed for single genome assembly and cannot be used to assemble and estimate the frequency of closely related quasispecies sequences. This work focuses on parsimonious and maximum likelihood models for assembling viral quasispecies and estimating their frequencies from 454 sequencing data. Ou
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Morlot, Jean-Baptiste. "Annotation of the human genome through the unsupervised analysis of high-dimensional genomic data." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066641/document.

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Le corps humain compte plus de 200 types cellulaires différents possédant une copie identique du génome mais exprimant un ensemble différent de gènes. Le contrôle de l'expression des gènes est assuré par un ensemble de mécanismes de régulation agissant à différentes échelles de temps et d'espace. Plusieurs maladies ont pour cause un dérèglement de ce système, notablement les certains cancers, et de nombreuses applications thérapeutiques, comme la médecine régénérative, reposent sur la compréhension des mécanismes de la régulation géniques. Ce travail de thèse propose, dans une première partie,
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Books on the topic "Genome reconstruction"

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Structure-Based Genome Scale Function Prediction and Reconstruction of the Mycobacterium tuberculosis Metabolic Network. [publisher not identified], 2014.

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Straalen, Nico, and Dick Roelofs. Human Evolution and Development. Amsterdam University Press, 2019. http://dx.doi.org/10.5117/9789463729208.

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Our understanding of human evolution is proceeding at an unprecedented rate over the last years due to spectacular fossil finds, reconstructions based on genome comparison, ancient DNA sequencing and new insights into developmental genetics. This book takes an integrative approach in which the development of the human embryo, the evolutionary history of our body, the structure of human populations, their dispersal over the world and their cultures are examined by integrating paleoanthropology, developmental biology, comparative zoology, population genetics and phylogenetic reconstruction. The
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1940-, Fink Carole, Frohn Axel 1952-, and Heideking Jürgen 1947-, eds. Genoa, Rapallo, and European reconstruction in 1922. German Historical Institute, 1991.

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Engineering peace: The military role in postconflict reconstruction. Institute of Peace Press, 2004.

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Iwanaga, Terumi, and Tomohiro Banno. "Tsukinami saireizu byōbu" no fukugen to kenkyū: Yomigaeru Muromachi Kyōto no kagayaki = The splendor of Muromachi Kyoto reborn : reconstructing Folding screens of the festivals of the twelve months. Shibunkaku Shuppan, 2020.

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The origins of detente: The Genoa Conference and Soviet-Western relations, 1921-1922. Cambridge University Press, 1985.

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The Genoa Conference: European diplomacy, 1921-1922. Syracuse University Press, 1993.

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Xiao, Fengxia. Reconstruction of the Evolution of Chinese Populations by the Study of Human Genome Diversity. Leuven Univ Pr, 2001.

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Kaplan, E. Ann. Troubling Genre/Reconstructing Gender. University of Illinois Press, 2017. http://dx.doi.org/10.5406/illinois/9780252036613.003.0005.

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This chapter explores the cultural work that feminist critics performed in “inventing” the genre of the woman's film, and how genre impacts on feminist cinema practices in the current postmodern moment. It argues first that historically, genre was important in providing a useful pathway through which feminist film theorists could assert a critical position vis-à-vis dominant cinematic and critical strategies. That is, feminist critics used genre as a concept to invent a new genre—the women's picture or woman's film—thereby drawing attention to aspects of Hollywood melodrama that had been negle
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Orthopaedic Knowledge Update®: Hip and Knee Reconstruction 6 Print + Ebook. AAOS, 2021.

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Book chapters on the topic "Genome reconstruction"

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Tang, Jijun. "Ancestral Genome Reconstruction." In Bioinformatics and Phylogenetics. Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-10837-3_9.

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Fondi, Marco, and Pietro Liò. "Genome-Scale Metabolic Network Reconstruction." In Methods in Molecular Biology. Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-1720-4_15.

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Sankoff, David, and Chunfang Zheng. "Fractionation, Rearrangement, Consolidation, Reconstruction." In Models and Algorithms for Genome Evolution. Springer London, 2013. http://dx.doi.org/10.1007/978-1-4471-5298-9_11.

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Dal’Molin, Cristiana G. O., and Lars K. Nielsen. "Algae Genome-Scale Reconstruction, Modelling and Applications." In The Physiology of Microalgae. Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-24945-2_22.

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Baart, Gino J. E., and Dirk E. Martens. "Genome-Scale Metabolic Models: Reconstruction and Analysis." In Methods in Molecular Biology. Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-346-2_7.

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Nakatani, Yoichiro, Hiroyuki Takeda, Yuji Kohara, and Shinichi Morishita. "Reconstruction of the Vertebrate Ancestral Genome Reveals Dynamic Genome Reorganization in Early Vertebrates." In Medaka. Springer Japan, 2011. http://dx.doi.org/10.1007/978-4-431-92691-7_20.

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Bertrand, Denis, Yves Gagnon, Mathieu Blanchette, and Nadia El-Mabrouk. "Reconstruction of Ancestral Genome Subject to Whole Genome Duplication, Speciation, Rearrangement and Loss." In Lecture Notes in Computer Science. Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-15294-8_7.

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Xu, Qiaoji, and David Sankoff. "Gene Order Phylogeny via Ancestral Genome Reconstruction Under Dollo." In Comparative Genomics. Springer Nature Switzerland, 2023. http://dx.doi.org/10.1007/978-3-031-36911-7_7.

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AbstractWe present a proof of principle for a new kind of stepwise algorithm for unrooted binary gene-order phylogenies. This method incorporates a simple look-ahead inspired by Dollo’s law, while simultaneously reconstructing each ancestor (sometimes referred to as hypothetical taxonomic units “HTU”). We first present a generic version of the algorithm illustrating a necessary consequence of Dollo characters. In a concrete application we use generalized oriented gene adjacencies and maximum weight matching (MWM) to reconstruct fragments of monoploid ancestral genomes as HTUs. This is applied to three flowering plant orders while estimating phylogenies for these orders in the process. We discuss how to improve on the extensive computing times that would be necessary for this method to handle larger trees.
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Masoudi-Nejad, Ali, Ali Salehzadeh-Yazdi, Shiva Akbari-Birgani, and Yazdan Asgari. "Integration of Metabolic Knowledge for Genome-Scale Metabolic Reconstruction." In Biological Knowledge Discovery Handbook. John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118617151.ch45.

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Zorrilla, Francisco, and Eduard J. Kerkhoven. "Reconstruction of Genome-Scale Metabolic Model for Hansenula polymorpha Using RAVEN." In Methods in Molecular Biology. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2399-2_16.

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Conference papers on the topic "Genome reconstruction"

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"Neurotransmitter gene network reconstruction and analisis." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-177.

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Zhou, Jun, Fei Hu, William Hoskins, and Jijun Tang. "Assessing ancestral genome reconstruction methods by resampling." In 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2014. http://dx.doi.org/10.1109/bibm.2014.6999377.

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"Gene network of type 2 diabetes: reconstruction and analysis." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-125.

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Li, YuTong. "Genome Reconstruction problem : By using De Bruijn graph." In 2021 International Conference on Artificial Intelligence, Big Data and Algorithms (CAIBDA). IEEE, 2021. http://dx.doi.org/10.1109/caibda53561.2021.00019.

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Bakos, Jason D., Panormitis E. Elenis, and Jijun Tang. "FPGA Acceleration of Phylogeny Reconstruction for Whole Genome Data." In 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering. IEEE, 2007. http://dx.doi.org/10.1109/bibe.2007.4375664.

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"Computer reconstruction of the ecological structure of intestinal microbiota communities based on high-throughput sequencing data." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-104.

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"Reconstruction and analysis of regulatory gene networks involving human genes associated with main forms of pathozoospermia." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-272.

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Lyman, Cole A., M. Stanley Fujimoto, Anton Suvorov, et al. "Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs." In 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE). IEEE, 2017. http://dx.doi.org/10.1109/bibe.2017.00-44.

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Subazini, Thankaswamy Kosalai, and Gopal Ramesh Kumar. "Reconstruction of genome-scale metabolic pathway in Aspergillus terreus NIH2624." In 2011 3rd International Conference on Electronics Computer Technology (ICECT). IEEE, 2011. http://dx.doi.org/10.1109/icectech.2011.5942064.

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"Reconstruction and analysis of potato Solanum tuberosum pangenome of Siberian cultivars." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-345.

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Reports on the topic "Genome reconstruction"

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Christopher Dupont, John Glass, Laura Sheahan, et al. Reconstruction of a Bacterial Genome from DNA Cassettes. Office of Scientific and Technical Information (OSTI), 2011. http://dx.doi.org/10.2172/1041049.

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Moret, Bernard M., and Tandy Warnow. Advances in Phylogeny Reconstruction from Gene Order and Content Data. Defense Technical Information Center, 2004. http://dx.doi.org/10.21236/ada482523.

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Elbaum, Michael, and Peter J. Christie. Type IV Secretion System of Agrobacterium tumefaciens: Components and Structures. United States Department of Agriculture, 2013. http://dx.doi.org/10.32747/2013.7699848.bard.

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Objectives: The overall goal of the project was to build an ultrastructural model of the Agrobacterium tumefaciens type IV secretion system (T4SS) based on electron microscopy, genetics, and immunolocalization of its components. There were four original aims: Aim 1: Define the contributions of contact-dependent and -independent plant signals to formation of novel morphological changes at the A. tumefaciens polar membrane. Aim 2: Genetic basis for morphological changes at the A. tumefaciens polar membrane. Aim 3: Immuno-localization of VirB proteins Aim 4: Structural definition of the substrate
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