Relevant bibliographies by topics / Pangenomics

Contents

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

Academic literature on the topic 'Pangenomics'

Author: Grafiati
Published: 10 May 2025

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Journal articles on the topic "Pangenomics"

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Durant, Éloi, François Sabot, Matthieu Conte, and Mathieu Rouard. "Panache: a web browser-based viewer for linearized pangenomes." Bioinformatics 37, no. 23 (October 2, 2021): 4556–58. http://dx.doi.org/10.1093/bioinformatics/btab688.

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Abstract Motivation Pangenomics evolved since its first applications on bacteria, extending from the study of genes for a given population to the study of all of its sequences available. While multiple methods are being developed to construct pangenomes in eukaryotic species there is still a gap for efficient and user-friendly visualization tools. Emerging graph representations come with their own challenges, and linearity remains a suitable option for user-friendliness. Results We introduce Panache, a tool for the visualization and exploration of linear representations of gene-based and sequence-based pangenomes. It uses a layout similar to genome browsers to display presence absence variations and additional tracks along a linear axis with a pangenomics perspective. Availability and implementation Panache is available at github.com/SouthGreenPlatform/panache under the MIT License.
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Llamas, Bastien, Giuseppe Narzisi, Valerie Schneider, Peter A. Audano, Evan Biederstedt, Lon Blauvelt, Peter Bradbury, et al. "A strategy for building and using a human reference pangenome." F1000Research 8 (July 29, 2021): 1751. http://dx.doi.org/10.12688/f1000research.19630.2.

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In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and standards for a usable human pangenome as well as to build relevant tools for genome graph infrastructures. During the meeting, the group held several intense and productive discussions covering a diverse set of topics, including advantages of graph genomes over a linear reference representation, design of new methods that can leverage graph-based data structures, and novel visualization and annotation approaches for pangenomes. Additionally, the participants self-organized themselves into teams that worked intensely over a three-day period to build a set of pipelines and tools for specific pangenomic applications. A summary of the questions raised and the tools developed are reported in this manuscript.
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Llamas, Bastien, Giuseppe Narzisi, Valerie Schneider, Peter A. Audano, Evan Biederstedt, Lon Blauvelt, Peter Bradbury, et al. "A strategy for building and using a human reference pangenome." F1000Research 8 (October 14, 2019): 1751. http://dx.doi.org/10.12688/f1000research.19630.1.

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In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and standards for a usable human pangenome as well as to build relevant tools for genome graph infrastructures. During the meeting, the group held several intense and productive discussions covering a diverse set of topics, including advantages of graph genomes over a linear reference representation, design of new methods that can leverage graph-based data structures, and novel visualization and annotation approaches for pangenomes. Additionally, the participants self-organized themselves into teams that worked intensely over a three-day period to build a set of pipelines and tools for specific pangenomic applications. A summary of the questions raised and the tools developed are reported in this manuscript.
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Golicz, Agnieszka A., Jacqueline Batley, and David Edwards. "Towards plant pangenomics." Plant Biotechnology Journal 14, no. 4 (November 23, 2015): 1099–105. http://dx.doi.org/10.1111/pbi.12499.

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Cho, Mildred K., Stephanie Malia Fullerton, Evelynn M. Hammonds, Sandra Soo-Jin Lee, Aaron Panofsky, and Jenny Reardon. "Pangenomics: prioritize diversity in collaborations." Nature 619, no. 7971 (July 25, 2023): 698. http://dx.doi.org/10.1038/d41586-023-02248-7.

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Baaijens, Jasmijn A., Paola Bonizzoni, Christina Boucher, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, and Jouni Sirén. "Computational graph pangenomics: a tutorial on data structures and their applications." Natural Computing 21, no. 1 (March 2022): 81–108. http://dx.doi.org/10.1007/s11047-022-09882-6.

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AbstractComputational pangenomics is an emerging research field that is changing the way computer scientists are facing challenges in biological sequence analysis. In past decades, contributions from combinatorics, stringology, graph theory and data structures were essential in the development of a plethora of software tools for the analysis of the human genome. These tools allowed computational biologists to approach ambitious projects at population scale, such as the 1000 Genomes Project. A major contribution of the 1000 Genomes Project is the characterization of a broad spectrum of genetic variations in the human genome, including the discovery of novel variations in the South Asian, African and European populations—thus enhancing the catalogue of variability within the reference genome. Currently, the need to take into account the high variability in population genomes as well as the specificity of an individual genome in a personalized approach to medicine is rapidly pushing the abandonment of the traditional paradigm of using a single reference genome. A graph-based representation of multiple genomes, or a graph pangenome, is replacing the linear reference genome. This means completely rethinking well-established procedures to analyze, store, and access information from genome representations. Properly addressing these challenges is crucial to face the computational tasks of ambitious healthcare projects aiming to characterize human diversity by sequencing 1M individuals (Stark et al. 2019). This tutorial aims to introduce readers to the most recent advances in the theory of data structures for the representation of graph pangenomes. We discuss efficient representations of haplotypes and the variability of genotypes in graph pangenomes, and highlight applications in solving computational problems in human and microbial (viral) pangenomes.
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Danilevicz, Monica Furaste, Cassandria Geraldine Tay Fernandez, Jacob Ian Marsh, Philipp Emanuel Bayer, and David Edwards. "Plant pangenomics: approaches, applications and advancements." Current Opinion in Plant Biology 54 (April 2020): 18–25. http://dx.doi.org/10.1016/j.pbi.2019.12.005.

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Aggarwal, Sumit Kumar, Alla Singh, Mukesh Choudhary, Aundy Kumar, Sujay Rakshit, Pardeep Kumar, Abhishek Bohra, and Rajeev K. Varshney. "Pangenomics in Microbial and Crop Research: Progress, Applications, and Perspectives." Genes 13, no. 4 (March 27, 2022): 598. http://dx.doi.org/10.3390/genes13040598.

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Advances in sequencing technologies and bioinformatics tools have fueled a renewed interest in whole genome sequencing efforts in many organisms. The growing availability of multiple genome sequences has advanced our understanding of the within-species diversity, in the form of a pangenome. Pangenomics has opened new avenues for future research such as allowing dissection of complex molecular mechanisms and increased confidence in genome mapping. To comprehensively capture the genetic diversity for improving plant performance, the pangenome concept is further extended from species to genus level by the inclusion of wild species, constituting a super-pangenome. Characterization of pangenome has implications for both basic and applied research. The concept of pangenome has transformed the way biological questions are addressed. From understanding evolution and adaptation to elucidating host–pathogen interactions, finding novel genes or breeding targets to aid crop improvement to design effective vaccines for human prophylaxis, the increasing availability of the pangenome has revolutionized several aspects of biological research. The future availability of high-resolution pangenomes based on reference-level near-complete genome assemblies would greatly improve our ability to address complex biological problems.
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Hu, Haifei, Jian Wang, Shuai Nie, Junliang Zhao, Jacqueline Batley, and David Edwards. "Plant pangenomics, current practice and future direction." Agriculture Communications 2, no. 2 (June 2024): 100039. http://dx.doi.org/10.1016/j.agrcom.2024.100039.

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Xiao, Jingfa, Zhewen Zhang, Jiayan Wu, and Jun Yu. "A Brief Review of Software Tools for Pangenomics." Genomics, Proteomics & Bioinformatics 13, no. 1 (February 2015): 73–76. http://dx.doi.org/10.1016/j.gpb.2015.01.007.

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Dissertations / Theses on the topic "Pangenomics"

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Ali, Amjad. "Comparative microbial genomics: pangenomics and pathogenomics of corynebacterium, campylobacter and helicobacter." Universidade Federal de Minas Gerais, 2013. http://hdl.handle.net/1843/BUOS-97PJMH.

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In the last decade, robust sequencing technologies have revolutionized the genomic science. As a result, comparative genomics is now recognized as a new discipline. Comparative microbial genomics exploits both similarities and differences in the genomes, proteome, trascriptome, and regulatory regions of different organisms to infer the evolutionary relations, along with conserved and unique characteristics of species. These analyses have resulted in some surprising biological discoveries in the recent past. This study presents comparative genomic analysis of multiple pathogenic and non-pathogenic bacteria from related species, to dissect the genomic information and to get insights into evolutionary relationships, conserved information and mechanisms of pathogenicity. Starting from genus Corynebacterium, 11 representative species are analysed and compared, resulting in 741 conserved Gene Families (GFs) in all of them, and significant intra-species proteome similarities (98-99%) were observed. Subsequently, the pan- (7059 GFs) and core genome (552 GFs) of genus Campylobacter is estimated. A detailed comparative pathogenomic study of Campylobacter fetus subspecies resulted in identification of common and novel regions associated with pathogenicity; and species specific virulence factors and vaccine candidates have been characterized. Furthermore, comparative genomics and pathogenomics analysis of the genus Helicobacter (46 genomes) is accomplished. 38 Helicobacter pylori were found to share 1,185 core gene families representing ~77% of the average genome size. The core essential genes families (EGFs) are ascertained, and explored for potential therapeutics against H. pylori. In conclusion, we propose that, these observed genomic variations, species specific features and core virulence factors will enhance understanding of the lifestyle of the organisms, and will contribute to the development of antibiotics, drugs and vaccines.
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SECOMANDI, SIMONA. "CHROMOSOME-LEVEL DE NOVO GENOME ASSEMBLIES OF AVIAN SPECIES AND THEIR RELEVANCE FOR COMPARATIVE GENOMICS, PANGENOMICS, POPULATION GENOMICS AND SPECIES CONSERVATION." Doctoral thesis, Università degli Studi di Milano, 2022. http://hdl.handle.net/2434/931506.

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Life on Earth is currently experiencing the sixth mass extinction. A major loss of species is being caused by anthropogenic habitat destruction, illegal wildlife trade, overfishing, massive fossil fuel consumption and the consequent climate changes, leading to a progressive collapse of biodiversity. The establishment of conservation initiatives is now more crucial than ever and the genetic management of threatened species is currently gaining critical significance. Previous genetic studies have been limited by the lack of complete reference genomes, thus having to focus on a limited number of genes or incomplete genomic sequencing data. In several cases, this led to wrong or incomplete assumptions and to conservation decisions which did not carry the desired effects due to incorrect evaluations. The availability of high-throughput sequencing technologies and the development of advanced computational methods have recently allowed the generation of cost-effective chromosome-level reference genomes. In the last decades, tremendous efforts were made to generate the most complete human genome. However, additional reference genomes spanning the entire tree of life are a necessary foundation for the study of biology in the 21st century, which was made possible with the establishment of large sequencing consortia. This thesis work represents a contribution to the collective effort of describing and preserving our planet's genetic diversity, being part of international consortia such as the Vertebrate Genomes Project (VGP), Darwin Tree of Life (DToL) and European Reference Genome Atlas (ERGA). Here I report new methods to assemble highly contiguous reference genomes for vertebrate species in the context of the VGP and their relevance in deciphering the biology of a species, its evolution, its intrinsic variability and in planning conservation actions, providing a comprehensive collection of genomic markers. Using the VGP pipelines, I have assembled 6 chromosome-level bird species: barn swallow (Hirundo rustica), lesser kestrel (Falco naumanni), American flamingo (Phoenicopterus ruber), common yellowthroat (Geothlypis trichas), rifleman (Acanthisitta chloris) and red-crested turaco (Tauraco erythrolophus), which fulfilled and exceeded the standard VGP metrics for genome assembly. Moreover, I contributed to the generation of the European nightjar (Caprimulgus europaeus) reference genome for the DToL. The genomes I generated will be exploited in the future to get insights into the biology of these species, but also for comparative genomics analyses using all available VGP-quality species. In particular, the lesser kestrel reference genome will be a fundamental resource for a future study that involves the assessment of how this species coped with climatic fluctuations in the past and how it is expected to cope with them in the future under the current scenario of climate changes. Moreover, the European nightjar genome will help to deepen the knowledge on the biology of this cryptic and 2 elusive bird, also boosting the sequencing of other members of the Caprimulgidae family to reconstruct a comprehensive phylogeny. During my PhD, I particularly focused on barn swallow (Hirundo rustica) genomics, an iconic migratory passerine bird with a long-standing association with humans. Using the VGP-quality assembly, I performed comparative genomics, population genomics and pangenomics analyses. Comparative genomics work was carried out with the reference-free aligner Cactus, with which I have aligned the barn swallow reference with other chromosome-level bird species. Using the alignment, I performed a positive and negative selection analysis across the genome to find candidate genes under selection important for barn swallow biology. For population genomics analyses, we aligned all publicly available data for the barn swallow subspecies and populations to the reference genome and performed a Linkage Disequilibrium scan. Comparative and population genomics approaches both pointed at candidate genes under selective constraint which may have a role in the onset of the synanthropic behavior of the species. Finally, with the reference genome and other HiFi-based barn swallow assemblies, I constructed the first pangenome graph for the species and preliminarily evaluated the extent of core and accessory genes among individuals. We also complemented the nuclear genome-based study with the generation of the complete mitochondrial genome for the species, which allowed us to dissect the phylogenetic relationships between barn swallow subspecies and to clarify the species’ phylogeographic history. In conclusion, this thesis work represents a valuable step forward and a contribution to international genome sequencing efforts. I outlined how complete genomic resources can revolutionize studies on the biology and evolution of a species, but also how they represent a pivotal resource to correctly plan threatened species conservation actions during the sixth mass extinction.
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Andreace, Francesco. "Analysis of human pangenome graphs : and other k-mer based applications." Electronic Thesis or Diss., Sorbonne université, 2025. http://www.theses.fr/2025SORUS017.

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Depuis plus de vingt ans, le génome Humain de référence a jeté les bases de la recherche en génomique Humaine. Toutefois, la quantité d'informations extraite de cette référence est limitée par sa non complétude et ses morceaux issus de simulations. En 2022, le consortium Telomere-to-Telomere a franchi une étape importante en publiant la première séquence complète d'un haploïde Humain(T2T-CHM13), ce qui a permis de faire de nouvelles découvertes sur les régions du génome qui étaient auparavant manquantes. Néanmoins, un seul génome ne peut pas représenter de manière adéquate l'ensemble de la diversité génétique au sein de la population Humaine, en particulier les grands variants structuraux. Pour remédier au biais de référence inhérent à l'utilisation d'un seul génome comme moyen de comparaison, la communauté scientifique s'oriente vers les pangénomes : il s'agit de modèles qui englobent de multiples allèles provenant d'une collection de génomes. Le domaine de la pangénomique computationnelle vise à trouver de nouveaux modèles de pangénomes plus efficaces qui peuvent améliorer les résultats des analyses basées sur les références. Entre autres, la représentation la plus courante du pangénome est basée sur les graphes. Cette thèse présente deux contributions principales à la pangénomique computationnelle. La première est une analyse comparative des représentations graphiques du pangénome, basée sur la construction du plus grand graphique du pangénome à ce jour. Cette analyse compare différents modèles de graphes, en utilisant cinq outils de pointe, mettant en lumière les principales différences entre les représentations, en particulier sur la façon dont elles capturent la variation génétique dans les loci complexes. La deuxième contribution porte sur les structures de données avancées pour la représentation des ensembles de k-mer. En particulier, trois nouvelles structures de données visent à améliorer l'association des métadonnées, l'accessibilité des analyses en aval et la scalabilité. Ces méthodes basées sur les kmer visent à faciliter les analyses génomiques et pangénomiques. Cette thèse présente ma contribution à l'évolution en cours de la recherche en pangénomique computationnelle
For over two decades, the human reference genome has laid the ground for human genomic research. However, its power to provide insights has been constrained by the presence of gaps and simulated sequences. In 2022, the Telomere-to-Telomere consortium achieved an important milestone by releasing the first full sequence of an haploid human genome (T2T-CHM13), empowering a new discoveries on the previously missing regions of the genome. Nevertheless, a single genome cannot adequately represent the entire genetic diversity within the human population, in particular large structural variants. To address the inherent reference bias of using a single genome as mean of comparison, the scientific community is transitioning towards pangenomes: these are models that encapsulate multiple alleles from a collection of genomes. The field of computational pangenomics aims at finding new and more efficient pangenome models that can improve the results of reference-based analyses. Among others, the most common pangenome representation is based on graphs. This dissertation presents two primary contributions to computational pangenomics. The first is a comparative analysis of pangenome graph representations, based on the construction of the largest pangenome graph to that date. This analysis compares different graph models, using five state-of-the-art tools, shed-ding light on key differences between the representation, particularly on how they capture genetic variation in complex loci. The second contribution focuses on advanced data structures for k-mer sets representation. In particular, on three novel data structures that focus on improving metadata association, downstream analysis accessibility and scalability. Thesek-mer-based methods aim at facilitating genomic and pangenomic analyses. This dissertation present my contributes to the ongoing evolution of computational pangenomics research
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Anani, Hussein. "La génomique bactérienne : un outil puissant pour la taxonomie et les analyses évolutives." Thesis, Aix-Marseille, 2020. http://theses.univ-amu.fr.lama.univ-amu.fr/200702_ANANI_94nya773wjmhky699k81cng_TH.pdf.

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La naissance de la génomique a révolutionné la classification des taxons bactériens. Actuellement, grâce au nombre élevé de génomes bactériens disponibles (> 250,000) et d'outils taxonomiques basés sur le génome, il est possible de réaliser des analyses phylogénomiques précises des bactéries pathogènes humaines. Au cours de notre thèse, nous avons d'abord mis en évidence l'intérêt des analyses pangénomiques en microbiologie clinique. De plus, la taxonomie des espèces de Bartonella, les agents de plusieurs maladies infectieuses humaines, étant mal connue, nous avons étudié 148 génomes de toutes les espèces de Bartonella afin de déterminer leur parenté génétique en utilisant plusieurs outils taxonomiques et généré leur premier pangénome. Par conséquent, nous avons défini des seuils spécifiques basés sur le génome pour la classification des isolats au niveau du genre et de l'espèce. De plus, en utilisant la stratégie culturomique, nous avons utilisé l'approche taxono-génomique pour décrire 25 nouveaux taxons bactériens isolés à partir d'un large éventail d'échantillons de différents pays. Nos résultats confirment donc qu'en 2020, la génomique permet de mettre à jour la taxonomie bactérienne traditionnelle et permet de mieux comprendre l'évolution bactérienne
The birth of genomics has revolutionized the classification of bacterial taxa. Currently, thanks to the high number of available bacterial genomes (> 250,000) and genome-based taxonomic tools, inferring accurate phylogenomic analyses of human pathogenic bacteria is achievable. During our thesis, we have first highlighted the usefulness of pangenomic analyses in clinical microbiology. In addition, since the taxonomy of Bartonella species, the agents of several human infectious diseases, is poorly understood, we have studied 148 genomes from all Bartonella species in order to determine their genetic relatedness by using several taxonomic tools and generated their first pangenome. Hence, we have defined specific genome-based thresholds for the classification of isolates at the genus and species levels. Furthermore, using the culturomics strategy, we used the taxono-genomics approach to describe 25 new bacterial taxa isolated from a wide spectrum of samples from different countries. Therefore, our results confirm that, in 2020, genomics enables updating the traditional bacterial taxonomy and help to better understand bacterial evolution
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Books on the topic "Pangenomics"

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Mengoni, Alessio, Giovanni Bacci, and Marco Fondi, eds. Bacterial Pangenomics. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1099-2.

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Mengoni, Alessio, Marco Galardini, and Marco Fondi, eds. Bacterial Pangenomics. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-1720-4.

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Fondi, Marco, Alessio Mengoni, and Marco Galardini. Bacterial pangenomics: Methods and protocols. New York, NY: Humana Press, 2015.

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Bacterial Pangenomics: Methods and Protocols. Springer, 2022.

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Fondi, Marco, Alessio Mengoni, and Marco Galardini. Bacterial Pangenomics: Methods and Protocols. Springer New York, 2016.

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Fondi, Marco, Giovanni Bacci, and Alessio Mengoni. Bacterial Pangenomics: Methods and Protocols. Springer, 2021.

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Book chapters on the topic "Pangenomics"

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Fernandez, Cassandria Tay, Jacob Marsh, Mônica Furaste Danilevicz, Clémentine Mercé, and David Edwards. "Application of pangenomics for wheat molecular breeding." In Molecular breeding in wheat, maize and sorghum: strategies for improving abiotic stress tolerance and yield, 236–46. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789245431.0013.

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Abstract This chapter discusses the application of pangenomics for molecular breeding of wheat. Pangenomes can be used by both researchers and breeders alike to develop elite wheat cultivars through the discovery and integration of genetic variations associated with agronomically beneficial traits. By providing a reference that accommodates for variation in individuals, variants whose presence and/or absence control abiotic stress resistance and yield can be identified. This tool has only become more informative as more wheat varieties are sequenced, new sequencing approaches such as long-read sequencing and genome mapping are utilized, and tools for pangenomic analysis are developed. With pangenomics, variable genes from wild wheat relatives and related species can be used to optimize wheat molecular breeding and develop improved varieties tailored for the changing global environment.
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Priyadharshini, S., P. Samuel, M. Gnanaraj, M. Bala Sundar, M. Rajadurai, D. Rajasudhakar, and T. Jebastin. "Pangenomes and Pangenomics in Medicinal Plants." In Biotechnology, Multiple Omics, and Precision Breeding in Medicinal Plants, 70–78. Boca Raton: CRC Press, 2025. https://doi.org/10.1201/9781003475491-6.

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Yildiz, Gözde, Silvia Zanini, Paul Knight, and Agnieszka A. Golicz. "Pangenomics in Agriculture." In Next-Generation Sequencing and Agriculture, 163–87. GB: CABI, 2022. http://dx.doi.org/10.1079/9781789247848.0008.

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Kiefer, Christiane. "Im Zeitalter von Genomsequenzierung und Pangenomics." In Genomevolution bei Pflanzen, 33–46. Wiesbaden: Springer Fachmedien Wiesbaden, 2021. http://dx.doi.org/10.1007/978-3-658-33025-5_6.

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Kahanda, Indika, Joann Mudge, Buwani Manuweera, Thiruvarangan Ramaraj, Alan Cleary, and Brendan Mumey. "Graph-Based Machine Learning Approaches for Pangenomics." In Machine Learning Methods for Multi-Omics Data Integration, 117–32. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-36502-7_7.

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Ma, Bing, Michael France, and Jacques Ravel. "Meta-Pangenome: At the Crossroad of Pangenomics and Metagenomics." In The Pangenome, 205–18. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-38281-0_9.

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Hu, Haifei, Monica Furaste Danilevicz, Chengdao Li, and David Edwards. "Pangenomics and Machine Learning in Improvement of Crop Plants." In Advances in Plant Breeding Strategies, 321–47. Cham: Springer Nature Switzerland, 2024. https://doi.org/10.1007/978-3-031-68586-6_12.

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Williams, Lucia, and Brendan Mumey. "Extending Maximal Perfect Haplotype Blocks to the Realm of Pangenomics." In Algorithms for Computational Biology, 41–48. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-42266-0_4.

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Bonizzoni, Paola, Clelia De Felice, Yuri Pirola, Raffaella Rizzi, Rocco Zaccagnino, and Rosalba Zizza. "Can Formal Languages Help Pangenomics to Represent and Analyze Multiple Genomes?" In Developments in Language Theory, 3–12. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-05578-2_1.

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Fagorzi, Camilla, and Alice Checcucci. "A Compendium of Bioinformatic Tools for Bacterial Pangenomics to Be Used by Wet-Lab Scientists." In Methods in Molecular Biology, 233–43. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1099-2_15.

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Conference papers on the topic "Pangenomics"

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Strang, Lilja Caitlin, and Craig Moyer. "INSIGHTS INTO THE PANGENOMICS OF DEEP SUBSURFACE THERMOCOCCUS ISOLATES." In GSA Annual Meeting in Seattle, Washington, USA - 2017. Geological Society of America, 2017. http://dx.doi.org/10.1130/abs/2017am-308295.

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Su, Hang, Ziwei Chen, Maya L. Najarian, Martin T. Ferris, Fernando Pardo-Manuel de Villena, and Leonard McMillan. "A k -mer query tool for assessing population diversity in pangenomes." In BCB '21: 12th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. New York, NY, USA: ACM, 2021. http://dx.doi.org/10.1145/3459930.3469537.

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Leonard, A. S., and H. Pausch. "251. Pangenomes of haplotype-resolved assemblies enable population-scale genotyping of cattle structural variation." In World Congress on Genetics Applied to Livestock Production. The Netherlands: Wageningen Academic Publishers, 2022. http://dx.doi.org/10.3920/978-90-8686-940-4_251.

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