Relevant bibliographies by topics / Ancestral genomes

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

Academic literature on the topic 'Ancestral genomes'

Author: Grafiati
Published: 4 June 2021
Last updated: 5 February 2022

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Journal articles on the topic "Ancestral genomes"

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Schaefer, Nathan K., Beth Shapiro, and Richard E. Green. "An ancestral recombination graph of human, Neanderthal, and Denisovan genomes." Science Advances 7, no. 29 (2021): eabc0776. http://dx.doi.org/10.1126/sciadv.abc0776.

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Many humans carry genes from Neanderthals, a legacy of past admixture. Existing methods detect this archaic hominin ancestry within human genomes using patterns of linkage disequilibrium or direct comparison to Neanderthal genomes. Each of these methods is limited in sensitivity and scalability. We describe a new ancestral recombination graph inference algorithm that scales to large genome-wide datasets and demonstrate its accuracy on real and simulated data. We then generate a genome-wide ancestral recombination graph including human and archaic hominin genomes. From this, we generate a map w
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RASCOL, V., P. PONTAROTTI, and A. LEVASSEUR. "Ancestral animal genomes reconstruction." Current Opinion in Immunology 19, no. 5 (2007): 542–46. http://dx.doi.org/10.1016/j.coi.2007.06.009.

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Lee, Daehwan, Jongin Lee, Woon-Young Hong, Eunji Jang, and Jaebum Kim. "AGB (Ancestral Genome Browser): A Web Interface for Browsing Reconstructed Ancestral Genomes." Journal of KIISE 42, no. 12 (2015): 1584–89. http://dx.doi.org/10.5626/jok.2015.42.12.1584.

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Xu, Qiaoji, Lingling Jin, James H. Leebens-Mack, and David Sankoff. "Validation of Automated Chromosome Recovery in the Reconstruction of Ancestral Gene Order." Algorithms 14, no. 6 (2021): 160. http://dx.doi.org/10.3390/a14060160.

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The RACCROCHE pipeline reconstructs ancestral gene orders and chromosomal contents of the ancestral genomes at all internal vertices of a phylogenetic tree. The strategy is to accumulate a very large number of generalized adjacencies, phylogenetically justified for each ancestor, to produce long ancestral contigs through maximum weight matching. It constructs chromosomes by counting the frequencies of ancestral contig co-occurrences on the extant genomes, clustering these for each ancestor and ordering them. The main objective of this paper is to closely simulate the evolutionary process givin
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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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Ouzounis, Christos A. "Ancestral state reconstructions for genomes." Current Opinion in Genetics & Development 15, no. 6 (2005): 595–600. http://dx.doi.org/10.1016/j.gde.2005.09.011.

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Jones, B. R., A. Rajaraman, E. Tannier, and C. Chauve. "ANGES: reconstructing ANcestral GEnomeS maps." Bioinformatics 28, no. 18 (2012): 2388–90. http://dx.doi.org/10.1093/bioinformatics/bts457.

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Pompidor, Nicolas, Carine Charron, Catherine Hervouet, et al. "Three founding ancestral genomes involved in the origin of sugarcane." Annals of Botany 127, no. 6 (2021): 827–40. http://dx.doi.org/10.1093/aob/mcab008.

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Abstract Background and Aims Modern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12x = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum. Methods To analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among repre
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Huang, Xiaosong, Laurent-Philippe Albou, Tremayne Mushayahama, Anushya Muruganujan, Haiming Tang, and Paul D. Thomas. "Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life." Nucleic Acids Research 47, no. D1 (2018): D271—D279. http://dx.doi.org/10.1093/nar/gky1009.

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Guyot, Romain, and Beat Keller. "Ancestral genome duplication in rice." Genome 47, no. 3 (2004): 610–14. http://dx.doi.org/10.1139/g04-016.

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The recent availability of the pseudochromosome sequences of rice allows for the first time the investigation of the extent of intra-genomic duplications on a large scale in this agronomically important species. Using a dot-matrix plotter as a tool to display pairwise comparisons of ordered predicted coding sequences along rice pseudochromosomes, we found that the rice genome contains extensive chromosomal duplications accounting for 53% of the available sequences. The size of duplicated blocks is considerably larger than previously reported. In the rice genome, a duplicated block size of >
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Dissertations / Theses on the topic "Ancestral genomes"

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Al-Nuaimi, Bashar. "Ancestral Reconstruction and Investigations of Genomics Recombination on Chloroplasts Genomes." Thesis, Bourgogne Franche-Comté, 2017. http://www.theses.fr/2017UBFCD042/document.

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La théorie de l’évolution repose sur la biologie moderne. Toutes les nouvelles espèces émergent d’une espèce existante. Il en résulte que différentes espèces partagent une ascendance commune, telle que représentée dans la classification phylogénétique. L’ascendance commune peut expliquer les similitudes entre tous les organismes vivants, tels que la chimie générale, la structure cellulaire, l’ADN comme matériau génétique et le code génétique. Les individus d’une espèce partagent les mêmes gènes mais (d’ordinaire) différentes séquences d’allèles de ces gènes. Un individu hérite des allèles de l
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Damas, Joana Daniela Mendes. "Avian genomics : from improvement of sequenced genomes to ancestral karyotypes and novel patterns of chromosomal evolution." Thesis, Royal Veterinary College (University of London), 2017. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.766310.

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Brozynska, Marta, Dario Copetti, Agnelo Furtado, et al. "Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice." WILEY, 2017. http://hdl.handle.net/10150/624392.

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The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that o
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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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Gutiérrez, Arumi Armand 1980. "Ancestral genomic submicroscopic inversions of human genome and their relation with multifactorial human diseases." Doctoral thesis, Universitat Pompeu Fabra, 2016. http://hdl.handle.net/10803/454777.

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Significant advances were performed in mapping and characterizing different types of structural variation in the human genome such as point mutations, insertions, deletions, etc. Nevertheless, there is still an important genetic component in multifactorial diseases that it is still unknown. Inversions are chromosome mutations in which a given loci change its orientation respect to a reference and present a balanced genetic material (neutral copy number). Our group developed tools in order to infer some variants of ancestral submicroscopic inversions (0.5 Mb – 5Mb) using computational methods w
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Brennan, Patrick J. "An Investigation of Personal Ancestry Using Haplotypes." University of Toledo / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1501705310326744.

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Crouch, Daniel. "Inferring ancestral and biogeographic origin using genome-wide SNP data." Thesis, King's College London (University of London), 2013. https://kclpure.kcl.ac.uk/portal/en/theses/inferring-ancestral-and-biogeographic-origin-using-genomewide-snp-data(e08f9863-9d91-48d2-a50f-f3fbee6269f1).html.

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Statistically predicting the origin of a human DNA sample has proven effective in forensic casework, and is of broad population genetic interest, but many facets of the problem remain unexplored. This thesis consolidates several pieces of work on the genetic prediction of origin; furthering its theory and practice. I begin by examining the performance of straightforward predictive methods when the objective is to correctly determine an individual's origin from one of several closely related genetic groups, e.g. countries within Europe. Of particular interest are the volume of data required to
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Jean, Géraldine. "In silico methods for genome rearrangement analysis : from identification of common markers to ancestral reconstruction." Thesis, Bordeaux 1, 2008. http://www.theses.fr/2008BOR13704/document.

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L'augmentation du nombre de génomes totalement séquencés rend de plus en plus efficace l'étude des mécanismes évolutifs à partir de la comparaison de génomes contemporains. L'un des principaux problèmes réside dans la reconstruction d'architectures de génomes ancestraux plausibles afin d'apporter des hypothèses à la fois sur l'histoire des génomes existants et sur les mécanismes de leur formation. Toutes les méthodes de reconstruction ancestrale ne convergent pas nécessairement vers les mêmes résultats mais sont toutes basées sur les trois mêmes étapes : l'identification des marqueurs communs
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Feiner, Nathalie [Verfasser]. "Characterization of cryptic components of the ancestral vertebrate genome / Nathalie Feiner." Konstanz : Bibliothek der Universität Konstanz, 2013. http://d-nb.info/1035067048/34.

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Zhao, Ziming. "Exploiting phylogenetics to understand genome evolution in both modern and ancestral organisms." Diss., Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/48988.

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Computational evolutionary analyses, particularly phylogenetics and ancestral reconstruction, have been extensively exploited under different algorithms and evolutionary models to better understand genome evolution from both small- and large-scale perspectives in order to assign genotypes based on assortment, resolve species relationships and gene annotation issues, further understand gene gain/loss within individual gene families, measure functional divergence among homologs, and infer ancestral character states. These evolutionary studies provide us with insights into biologically relevant i
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Books on the topic "Ancestral genomes"

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Racial identities, genetic ancestry, and health in South America: Argentina, Brazil, Colombia, and Uruguay. Palgrave Macmillan, 2011.

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GIBBON, SAHRA, Ricardo Ventura Santos, and Mónica Sans. Racial identities, genetic ancestry, and health in South America: Argentina, Brazil, Colombia, and Uruguay. Palgrave Macmillan, 2011.

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Hochschild, Jennifer. Genomic Politics. Oxford University Press, 2021. http://dx.doi.org/10.1093/oso/9780197550731.001.0001.

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Genomic science is moving out of the laboratory and into societal uses: gene therapy for terrible diseases, evidence determining guilt or innocence in a courtroom, exploration of one’s racial and ethnic ancestry, prenatal testing, and much more. Genomics promises great benefits. It also entails great risks: surveillance, a revival of eugenics, the threat of bioterrorism, and the distortions brought about by understanding life as mechanically determined rather than freely chosen.
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Irving, Melita. Human DNA Manual : Understanding Your Genetic Code: Evolution * Ancestry * Health * Genomics * Epigenetics. Haynes Publishing Group P.L.C., 2019.

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Scodari, Christine. Alternate Roots. University Press of Mississippi, 2018. http://dx.doi.org/10.14325/mississippi/9781496817785.001.0001.

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For over two decades, the media have chronicled escalating participation in family history prompted by, among other things, the aging of Baby Boomers and Generation Xers, the growing availability of digital genealogy sites and archives, and a burgeoning interest in racial and ethnic history and culture of the sort inspired by the airing of the historical drama miniseries Roots forty years ago. Alternate Roots is the first book to critically address a wide array of media-related institutions, texts, technologies, and practices of family history readily encountered in the new millennium, includi
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Phillips, Andelka M. Buying your Self on the Internet. Edinburgh University Press, 2019. http://dx.doi.org/10.3366/edinburgh/9781474422598.001.0001.

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The personal genomics industry (aka direct-to-consumer genetic testing) has created a market for genetic tests as consumer services. This has taken genetic testing out of the clinic and into people’s homes. The industry is diverse offering tests for various health conditions and ancestry, as well as more dubious tests, such as ‘peace of mind’ paternity, ‘infidelity’ (or surreptitious testing), child talent, and even matchmaking. It is growing rapidly, but at present many tests are not standardized and the industry has not been subject to specific regulation. As with many other Internet based i
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Tangen, Catherine M., Marian L. Neuhouser, and Janet L. Stanford. Prostate Cancer. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780190238667.003.0053.

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Prostate cancer is the most common solid tumor and the second leading cause of cancer-related mortality in American men. Worldwide, prostate cancer ranks second and fifth as a cause of cancer and cancer deaths, respectively. Despite the international burden of disease due to prostate cancer, its etiology is unclear in most cases. Established risk factors include age, race/ancestry, and family history of the disease. Prostate cancer has a strong heritable component, and genome-wide association studies have identified over 110 common risk-associated genetic variants. Family-based sequencing stud
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Hart, Anne. Nutritional Genomics - A Consumer's Guide to How Your Genes and Ancestry Respond to Food: Tailoring What You Eat to Your DNA. iUniverse, 2003.

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Book chapters on the topic "Ancestral genomes"

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Li, Guoliang, Jian Ma, and Louxin Zhang. "Selecting Genomes for Reconstruction of Ancestral Genomes." In Comparative Genomics. Springer Berlin Heidelberg, 2007. http://dx.doi.org/10.1007/978-3-540-74960-8_9.

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Tang, Jijun, and David A. Bader. "Phylogenetic and Ancestral Reconstruction of Multichromosomal Genomes." In Encyclopedia of Systems Biology. Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_967.

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Cheng, Feng, Martin A. Lysak, Terezie Mandáková, and Xiaowu Wang. "The Common Ancestral Genome of the Brassica Species." In Compendium of Plant Genomes. Springer Berlin Heidelberg, 2015. http://dx.doi.org/10.1007/978-3-662-47901-8_8.

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Gao, Zhihong, and Shahid Iqbal. "Reconstruction of Ancestral Chromosomes of the Family Rosaceae." In Compendium of Plant Genomes. Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-10797-0_14.

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Moore, Graham. "Comparative Cereal Genome Analysis-Reconstructing the Ancestral Cereal Genome." In Genomes of Plants and Animals. Springer US, 1996. http://dx.doi.org/10.1007/978-1-4899-0280-1_12.

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Collins, Caitlin, and Xavier Didelot. "Reconstructing the Ancestral Relationships Between Bacterial Pathogen Genomes." In Methods in Molecular Biology. Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6673-8_8.

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Guyeux, Christophe, Bashar Al-Nuaimi, Bassam AlKindy, Jean-François Couchot, and Michel Salomon. "On the Ability to Reconstruct Ancestral Genomes from Mycobacterium Genus." In Bioinformatics and Biomedical Engineering. Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-56148-6_57.

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Jin, Wenfei. "Distribution of Length of Ancestral Chromosomal Segments in Admixed Genomes." In Admixture Dynamics, Natural Selection and Diseases in Admixed Populations. Springer Netherlands, 2015. http://dx.doi.org/10.1007/978-94-017-7408-6_2.

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Stanyon, Roscoe, Gary Stone, and Francesca Bigoni. "The Ancestral Genomes in Primate Phylogeny and Origins: A Molecular Cytogenetic Perspective." In Anthropoid Origins. Springer US, 2004. http://dx.doi.org/10.1007/978-1-4419-8873-7_4.

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Earnest-DeYoung, Joel V., Emmanuelle Lerat, and Bernard M. E. Moret. "Reversing Gene Erosion – Reconstructing Ancestral Bacterial Genomes from Gene-Content and Order Data." In Lecture Notes in Computer Science. Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-30219-3_1.

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Conference papers on the topic "Ancestral genomes"

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Avdeyev, Pavel, and Max A. Alekseyev. "Linearization of Ancestral Genomes with Duplicated Genes." In BCB '20: 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. ACM, 2020. http://dx.doi.org/10.1145/3388440.3412484.

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Phuong Thao, Nguyen Thi, and Le Sy Vinh. "Building minimum recombination ancestral recombination graphs for whole genomes." In 2017 4th NAFOSTED Conference on Information and Computer Science. IEEE, 2017. http://dx.doi.org/10.1109/nafosted.2017.8108072.

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Yang, Kuan, and Joao C. Setubal. "Homology prediction refinement and reconstruction of gene content and order of ancestral bacterial genomes." In the First ACM International Conference. ACM Press, 2010. http://dx.doi.org/10.1145/1854776.1854810.

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Qu, Yue, Dat Tran, and Elisa Martinez-Marroquin. "Biogeographical Ancestry Inference from Genotype: A Comparison of Ancestral Informative SNPs and Genome-wide SNPs." In 2020 IEEE Symposium Series on Computational Intelligence (SSCI). IEEE, 2020. http://dx.doi.org/10.1109/ssci47803.2020.9308171.

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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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Ma, Jian. "A probabilistic framework for inferring ancestral genomic orders." In 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2010. http://dx.doi.org/10.1109/bibm.2010.5706559.

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MORET, BERNARD M. E., WEBB MILLER, PAVEL A. PEVZNER, and DAVID SANKOFF. "COMPUTATIONAL CHALLENGES IN COMPARATIVE GENOMICS: GENE FAMILY EVOLUTION, ANCESTRAL GENOME RECONSTRUCTION, AND APPLICATIONS TO HUMAN GENETICS – SESSION INTRODUCTION." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2008. http://dx.doi.org/10.1142/9789812836939_0011.

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Malmer, Daniel, Phillip Richmond, Aaron Odell, Richard Radcliffe, and Robin Dowell. "Inferring ancestry in mouse genomes using a hidden Markov model." In BCB '14: ACM-BCB '14. ACM, 2014. http://dx.doi.org/10.1145/2649387.2660812.

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Miyashita, Minoru, Joshua SK Bell, Yonglan Zheng, et al. "Abstract SS1-04: Comprehensive genomic and transcriptomic profiling of molecular subtypes reveal ancestral differences in the activity of signaling pathways between patients with African and European ancestry." In Abstracts: 2020 San Antonio Breast Cancer Virtual Symposium; December 8-11, 2020; San Antonio, Texas. American Association for Cancer Research, 2021. http://dx.doi.org/10.1158/1538-7445.sabcs20-ss1-04.

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Baye, Tesfaye Mersha. "Abstract 2746: Genomic data mining for selecting informative markers for ancestry." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-2746.

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Reports on the topic "Ancestral genomes"

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Reid, Robyn. Analyzing Riboswitches as a Function of Genome Size and Genus Ancestry in Gammaproteobacteria. Portland State University Library, 2015. http://dx.doi.org/10.15760/honors.191.

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