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Relevant bibliographies by topics / Genome comparison

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Academic literature on the topic 'Genome comparison'

Author: Grafiati

Published: 4 June 2021

Last updated: 10 March 2023

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Journal articles on the topic "Genome comparison"

1

Flanagan, Keith, Robert Stevens, Matthew Pocock, Pete Lee, and Anil Wipat. "Ontology for Genome Comparison and Genomic Rearrangements." Comparative and Functional Genomics 5, no. 6-7 (2004): 537–44. http://dx.doi.org/10.1002/cfg.436.

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We present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature defined by the ontology will foster clearer communication between biologists, and also standardize terms used by data publishers in the results of analysis programs. The overriding aim of this ontology is the facilitation of consistent annotation of genomes through computational methods, rather than human annotators. To this end, the ontology includes definitions that support computer analysis and automated transfer of annotations between genomes, rather than relying upon human mediation.

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Mori, K., K. Horimoto, S. Fukuchi, and K. Nishikawa. "Genome comparison based on gene locations : I Comparison between microbial genomes." Seibutsu Butsuri 41, supplement (2001): S81. http://dx.doi.org/10.2142/biophys.41.s81_1.

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Uras, Tansel, and Esra Erdem. "Genome Rearrangement and Planning: Revisited." Proceedings of the International Conference on Automated Planning and Scheduling 20 (May 25, 2021): 250–53. http://dx.doi.org/10.1609/icaps.v20i1.13434.

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Evolutionary trees of species can be reconstructed by pairwise comparison of their entire genomes. Such a comparison can be quantified by determining the number of events that change the order of genes in a genome. Earlier Erdem and Tillier formulated the pairwise comparison of entire genomes as the problem of planning rearrangement events that transform one genome to the other. We reformulate this problem as a planning problem to extend its applicability to genomes with multiple copies of genes and with unequal gene content, and illustrate its applicability and effectiveness on three real datasets: mitochondrial genomes of Metazoa, chloroplast genomes of Campanulaceae, chloroplast genomes of various land plants and green algae.

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Uras, Tansel, and Esra Erdem. "Genome Rearrangement: A Planning Approach." Proceedings of the AAAI Conference on Artificial Intelligence 24, no. 1 (July 5, 2010): 1963–64. http://dx.doi.org/10.1609/aaai.v24i1.7787.

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Evolutionary trees of species can be reconstructed by pairwise comparison of their entire genomes. Such a comparison can be quantified by determining the number of events that change the order of genes in a genome. Earlier Erdem and Tillier formulated the pairwise comparison of entire genomes as the problem of planning rearrangement events that transform one genome to the other. We reformulate this problem as a planning problem to extend its applicability to genomes with multiple copies of genes and with unequal gene content, and illustrate its applicability and effectiveness on three real datasets: mitochondrial genomes of Metazoa, chloroplast genomes of Campanulaceae, chloroplast genomes of various land plants and green algae.

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Bao, Jingyue, Yong Zhang, Chuan Shi, Qinghua Wang, Shujuan Wang, Xiaodong Wu, Shengbo Cao, Fengping Xu, and Zhiliang Wang. "Genome-Wide Diversity Analysis of African Swine Fever Virus Based on a Curated Dataset." Animals 12, no. 18 (September 16, 2022): 2446. http://dx.doi.org/10.3390/ani12182446.

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African swine fever (ASF) is a lethal contagious viral disease of domestic pigs and wild boars caused by the African swine fever virus (ASFV). The pandemic spread of ASF has had serious effects on the global pig industry. Virus genome sequencing and comparison play an important role in tracking the outbreaks of the disease and tracing the transmission of the virus. Although more than 140 ASFV genome sequences have been deposited in the public databases, the genome-wide diversity of ASFV remains unclear. Here we prepared a curated dataset of ASFV genome sequences by filtering genomes with sequencing errors as well as duplicated genomes. A total of 123 ASFV genome sequences were included in the dataset, representing 10 genotypes collected between 1949 and 2020. Phylogenetic analysis based on whole-genome sequences provided high-resolution topology in differentiating closely related ASFV isolates, and drew new clues in the classification of some ASFV isolates. Genome-wide diversity of ASFV genomes was explored by pairwise sequence similarity comparison and ORF distribution comparison. Tandem repeat sequences were found widely distributed and highly varied in ASFV genomes. Structural variation and highly variable poly G or poly C tracts also contributed to the genome diversity. This study expanded our knowledge on the patterns of genetic diversity and evolution of ASFV, and provided valuable information for diagnosis improvement and vaccine development.

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LAM, WINNIE W. M., KEITH C. C. CHAN, DAVID K. Y. CHIU, and ANDREW K. C. WONG. "A GRAPH-BASED ALGORITHM FOR MINING MULTI-LEVEL PATTERNS IN GENOMIC DATA." Journal of Bioinformatics and Computational Biology 08, no. 05 (October 2010): 789–807. http://dx.doi.org/10.1142/s0219720010005002.

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Comparative genomics is concerned with the study of genome structure and function of different species. It can provide useful information for the derivation of evolutionary and functional relationships between genomes. Previous work on genome comparison focuses mainly on comparing the entire genomes for visualization without further analysis. As many interesting patterns may exist between genomes and may lead to the discovering of functional gene segments (groups of genes), we propose an algorithm called Multi-Level Genome Comparison Algorithm (MGC) that can be used to facilitate the analysis of genomes at multi-levels during the comparison process to discover sequential and regional consistency in gene segments. Different genomes may have common sub-sequences that differ from each other due to mutations, lateral gene transfers, gene rearrangements, etc., and these sub-sequences are usually not easily identified. Not all the genes can have a perfect one-to-one matching with each other. It is quite possible for one-to-many or many-to-many ambiguous relationships to exist between them. To perform the tasks effectively, MGC takes such ambiguity into consideration during genome comparison by representing genomes in a graph and then make use of a graph mining algorithm called the Multi-Level Attributed Graph Mining Algorithm (MAGMA) to build a hierarchical multi-level graph structure to facilitate genome comparison. To determine the effectiveness of these proposed algorithms, experiments were performed using intra- and inter-species of Microbial genomes. The results show that the proposed algorithms are able to discover multiple level matching patterns that show the similarities and dissimilarities among different genomes, in addition to confirming the specific role of the genes in the genomes.

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Digiampietri, Luciano Antonio, Vivian Mayumi Yamassaki Pereira, Geraldo José Santos-Júnior, Giovani Sousa-Leite, Priscilla Koch Wagner, Leandro Márcio Moreira, and Caio Rafael do Nascimento Santiago. "A gene based bacterial whole genome comparison toolkit." Revista de Informática Teórica e Aplicada 26, no. 1 (April 14, 2019): 36. http://dx.doi.org/10.22456/2175-2745.84814.

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Most of the computational biology analysis is made comparing genomic features. The nucleotide and amino acid sequence alignments are frequently used in gene function identification and genome comparison. Despite its widespread use, there are limitations in their analysis capabilities that need to be considered but are often overlooked or unknown by many researchers. This paper presents a gene based whole genome comparison toolkit which can be used not only as an alternative and more robust way to compare a set of whole genomes, but, also, to understand the tradeoff of the use of sequence local alignment in this kind of comparison. A study case was performed considering fifteen whole genomes of the Xanthomonas genus. The results were compared with the 16S rRNA-processing protein RimM phylogeny and some thresholds for the use of sequence alignments in this kind of analysis were discussed.

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Tanaka, Mami, Sayaka Mino, Yoshitoshi Ogura, Tetsuya Hayashi, and Tomoo Sawabe. "Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case." PeerJ 6 (June 18, 2018): e5018. http://dx.doi.org/10.7717/peerj.5018.

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Whole genome sequence comparisons have become essential for establishing a robust scheme in bacterial taxonomy. To generalize this genome-based taxonomy, fast, reliable, and cost-effective genome sequencing methodologies are required. MinION, the palm-sized sequencer from Oxford Nanopore Technologies, enables rapid sequencing of bacterial genomes using minimal laboratory resources. Here we tested the ability of Nanopore sequences for the genome-based taxonomy of Vibrionaceae and compared Nanopore-only assemblies to complete genomes of five Rumoiensis clade species: Vibrio aphrogenes, V. algivorus, V. casei, V. litoralis, and V. rumoiensis. Comparison of overall genome relatedness indices (OGRI) and multilocus sequence analysis (MLSA) based on Nanopore-only assembly and Illumina or hybrid assemblies revealed that errors in Nanopore-only assembly do not influence average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), G+C content, or MLSA tree topology in Vibrionaceae. Our results show that the genome sequences from Nanopore-based approach can be used for rapid species identification based on the OGRI and MLSA.

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Rouchka, E. C. "Comparison of whole genome assemblies of the human genome." Nucleic Acids Research 30, no. 22 (November 15, 2002): 5004–14. http://dx.doi.org/10.1093/nar/gkf633.

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Sullivan, M. J., N. K. Petty, and S. A. Beatson. "Easyfig: a genome comparison visualizer." Bioinformatics 27, no. 7 (January 28, 2011): 1009–10. http://dx.doi.org/10.1093/bioinformatics/btr039.

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Dissertations / Theses on the topic "Genome comparison"

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Mok, Kwai-lung. "Computational discovery of cis-regulatory modules in human genome by genome comparison." Click to view the E-thesis via HKUTO, 2008. http://sunzi.lib.hku.hk/hkuto/record/b40203621.

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Mok, Kwai-lung, and 莫貴龍. "Computational discovery of cis-regulatory modules in human genome by genome comparison." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2008. http://hub.hku.hk/bib/B40203621.

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Dörr, Daniel [Verfasser]. "Gene family-free genome comparison / Daniel Dörr." Bielefeld : Universitätsbibliothek Bielefeld, 2016. http://d-nb.info/1096457229/34.

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Zerbino, Daniel Robert. "Genome assembly and comparison using de Bruijn graphs." Thesis, University of Cambridge, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611752.

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Sturgill, David Matthew. "Comparative Genome Analysis of Three Brucella spp. and a Data Model for Automated Multiple Genome Comparison." Thesis, Virginia Tech, 2003. http://hdl.handle.net/10919/10163.

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Comparative analysis of multiple genomes presents many challenges ranging from management of information about thousands of local similarities to definition of features by combination of evidence from multiple analyses and experiments. This research represents the development stage of a database-backed pipeline for comparative analysis of multiple genomes. The genomes of three recently sequenced species of Brucella were compared and a superset of known and hypothetical coding sequences was identified to be used in design of a discriminatory genomic cDNA array for comparative functional genomics experiments. Comparisons were made of coding regions from the public, annotated sequence of B. melitensis (GenBank) to the annotated sequence of B. suis (TIGR) and to the newly-sequenced B. abortus (personal communication, S. Halling, National Animal Disease Center, USDA). A systematic approach to analysis of multiple genome sequences is described including a data model for storage of defined features is presented along with necessary descriptive information such as input parameters and scores from the methods used to define features. A collection of adjacency relationships between features is also stored, creating a unified database that can be mined for patterns of features which repeat among or within genomes. The biological utility of the data model was demonstrated by a detailed analysis of the multiple genome comparison used to create the sample data set. This examination of genetic differences between three Brucella species with different virulence patterns and host preferences enabled investigation of the genomic basis of virulence. In the B. suis genome, seventy-one differentiating genes were found, including a contiguous 17.6 kb region unique to the species. Although only one unique species-specific gene was identified in the B. melitensis genome and none in the B. abortus genome, seventy-nine differentiating genes were found to be present in only two of the three Brucella species. These differentiating features may be significant in explaining differences in virulence or host specificity. RT-PCR analysis was performed to determine whether these genes are transcribed in vitro. Detailed comparisons were performed on a putative B. suis pathogenicity island (PAI). An overview of these genomic differences and discussion of their significance in the context of host preference and virulence is presented.
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Garg, Kavita. "Genome-wide comparison of evolutionarily conserved alternative and constitutive splice sites /." Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/10260.

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Wang, Hao. "THE POTENTIAL INDUCING PATTERN OF THE FLAX GENOME." Case Western Reserve University School of Graduate Studies / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=case1532609009820723.

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Vorster, Barend Juan. "Using whole genome comparison to detect sequence similarities between plants and microbes." Electronic thesis, 2007. http://upetd.up.ac.za/thesis/available/etd-01192009-142048.

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Bennett, Helen Victoria. "Giardia lamblia : a genome comparison of three reference strains using microarray technology." Thesis, Royal Holloway, University of London, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.538294.

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Lantermann, Alexandra. "Comparison of Genome-Wide Nucleosome Positioning Mechanisms in Schizosaccharomyces pombe and Saccharomyces cerevisiae." Diss., lmu, 2010. http://nbn-resolving.de/urn:nbn:de:bvb:19-118784.

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Books on the topic "Genome comparison"

1

Silance, Robert. Eight piazzas in Genoa, Italy: A comparison of form and scale. Charleston, S.C: Published for Clemson University College of Architecture, Arts and Humanities by Wyrick & Co., 1996.

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Silance, Robert. Eight piazzas in Genoa, Italy: A comparison of form and scale. Charlston, S.C: Published for Clemson University College of Architecture, Arts and Humanities by Wyrick & Co., 1996.

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Straalen, Nico, and Dick Roelofs. Human Evolution and Development. NL Amsterdam: 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 authors discuss questions like: - What do we know about ancient humans? - What happens in the development of an embryo? - How did we manage to walk upright and why did we lose our hair? - What is the relationship between language, migration and evolution? - How does our body respond to the challenges of modern society? In addition to being a core text for the study of the life sciences, Human Evolution and Development is an easy-to-read overview for the interested layperson.

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The Masks of God. Harmondsworth (Middlesex): Penguin Books, 1986.

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The masks of God. Markham, ON: Penguin Books, 1991.

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Joseph, Campbell. The masks of God. New York: Arkana, 1991.

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Gunnels, John A. A comparison of simulated annealing and genetic algorithms for the genome mapping problems. 1993.

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Epstein-Levi, Rebecca J. Intertextually Modified Organisms. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780190456023.003.0011.

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The chapter examines genetic engineering through analogy with the Torah: if Judaism permits rabbis, in some very specific circumstances, to alter the text of the sacred Torah, might it not also permit alteration of the “sacred text” of a plant’s genome? The chapter carefully plots these specific circumstances and their plant-based analogues to argue, with a comparison of genetic and scriptural languages, for respectful “dialogical engagement” to promote human and nonhuman flourishing. While not offering a clear answer to a challenging issue, the purpose is to establish the beginning of a religiously and textually attentive ethical framework with which to evaluate genetic technology.

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Siderits, Mark. Comparison or Confluence In Philosophy? Edited by Jonardon Ganeri. Oxford University Press, 2015. http://dx.doi.org/10.1093/oxfordhb/9780199314621.013.5.

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This chapter examines the project of fusion or confluence philosophy: philosophizing that draws on resources from both Indian and Western philosophical traditions in seeking solutions to philosophical problems. A distinction is drawn between the confluence project and the project of comparative philosophy. Various challenges to the project are addressed, among them the criticism that the two traditions are incommensurable, and the charge that such a project is politically problematic. There is also discussion of some ways in which projects of this sort can go astray. Representative samples of the genre are discussed, and areas that might prove promising for future research are identified.

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Rayner, Arthur Graham *. The comparison of unidentified open reading frames in the liverwort, tobacco, and "Vicia faba" chloroplast genomes. 1988.

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Book chapters on the topic "Genome comparison"

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Doerr, Daniel, Pedro Feijão, and Jens Stoye. "Family-Free Genome Comparison." In Comparative Genomics, 331–42. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7463-4_12.

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Wassenaar, T. M., J. Bohlin, T. T. Binnewies, and D. W. Ussery. "Genome Comparison of Bacterial Pathogens." In Microbial Pathogenomics, 1–20. Basel: KARGER, 2009. http://dx.doi.org/10.1159/000235759.

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Mudziwapasi, Reagan, Ringisai Chekera, Clophas Zibusiso Ncube, Irvonnie Shoko, Berlinda Ncube, Thandanani Moyo, Jeffrey Godfrey Chimbo, et al. "Comparison of ZFNs, TALENs, CRISPR, and MegaTALs." In Genome Editing Tools and Gene Drives, 45–50. Boca Raton: CRC Press, 2021. http://dx.doi.org/10.1201/9781003165316-6.

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Pabinger, Stephan, and Zlatko Trajanoski. "Genome-Scale Model Management and Comparison." In Methods in Molecular Biology, 3–16. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-299-5_1.

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Kuravadi, Nagesh A., and Malali Gowda. "Comparison of Gene Families and Synteny Analysis from Neem Genome." In The Neem Genome, 93–97. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-16122-4_10.

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Joshi, Jaya, Sudhakar Pandurangan, Marwan Diapari, and Frédéric Marsolais. "Comparison of Gene Families: Seed Storage and Other Seed Proteins." In The Common Bean Genome, 201–17. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-63526-2_10.

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Braga, Marília D. V., Cedric Chauve, Daniel Doerr, Katharina Jahn, Jens Stoye, Annelyse Thévenin, and Roland Wittler. "The Potential of Family-Free Genome Comparison." In Models and Algorithms for Genome Evolution, 287–307. London: Springer London, 2013. http://dx.doi.org/10.1007/978-1-4471-5298-9_13.

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Comin, Matteo, and Davide Verzotto. "Alignment-Free Measures for Whole-Genome Comparison." In Pattern Recognition in Computational Molecular Biology, 43–64. Hoboken, NJ, USA: John Wiley & Sons, Inc, 2015. http://dx.doi.org/10.1002/9781119078845.ch3.

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Jay, Jeremy J., John D. Eblen, Yun Zhang, Mikael Benson, Andy D. Perkins, Arnold M. Saxton, Brynn H. Voy, Elissa J. Chesler, and Michael A. Langston. "A Systematic Comparison of Genome Scale Clustering Algorithms." In Bioinformatics Research and Applications, 416–27. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-21260-4_39.

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Ramos, Lucas P., Felipe A. Louza, and Guilherme P. Telles. "Genome Comparison on Succinct Colored de Bruijn Graphs." In String Processing and Information Retrieval, 165–77. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-20643-6_12.

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Conference papers on the topic "Genome comparison"

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Othman, A., A. Martin, D. Butterstein, and M. I. Abouelhoda. "VisCHAINER: Visualizing Genome Comparison." In 2008 Cairo International Biomedical Engineering Conference (CIBEC). IEEE, 2008. http://dx.doi.org/10.1109/cibec.2008.4786044.

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Mednis, Martins, Valters Brusbardis, and Vytautas Galvanauskas. "Comparison of genome-scale reconstructions using ModeRator." In 2012 IEEE 13th International Symposium on Computational Intelligence and Informatics (CINTI). IEEE, 2012. http://dx.doi.org/10.1109/cinti.2012.6496737.

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Chateau, Annie, Pierre Riou, and Eric Rivals. "Approximate Common Intervals in Multiple Genome Comparison." In 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2011. http://dx.doi.org/10.1109/bibm.2011.96.

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Henley, Morel, Mikkel Hagen, and R. Daniel Bergeron. "Evaluating Two Visualization Techniques for Genome Comparison." In 2007 11th International Conference Information Visualization (IV '07). IEEE, 2007. http://dx.doi.org/10.1109/iv.2007.47.

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"Phylostratigraphic approach in evolutionary analysis: comparison of methods." 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-2020-141.

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"Peak caller comparison through quality control of ChIP-Seq datasets." 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-2020-065.

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"Accuracy of disorder predictors results – comparison on DisProt DB 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-2020-379.

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choi, Kwangmin, Amit Saple, and Sun Kim. "Genome Data Type: a Vehicle to Deliver a Genome Comparison System on the Web." In Sixth IEEE International Conference on Data Mining - Workshops (ICDMW'06). IEEE, 2006. http://dx.doi.org/10.1109/icdmw.2006.87.

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Baichoo, Shakuntala, Parinita Ujoodha, and Yovish Bissessur. "GCVT — A Genome Comparison and Viewing Tool." In 2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE). IEEE, 2012. http://dx.doi.org/10.1109/bibe.2012.6399708.

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Jacob, Arpith, Sugata Sanyal, Marcin Paprzycki, Rajan Arora, and Maria Ganzha. "Whole Genome Comparison on a Network of Workstations." In Sixth International Symposium on Parallel and Distributed Computing (ISPDC'07). IEEE, 2007. http://dx.doi.org/10.1109/ispdc.2007.58.

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Reports on the topic "Genome comparison"

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Serres, Margrethe H. Functional Analysis of Shewanella, a cross genome comparison. Office of Scientific and Technical Information (OSTI), May 2009. http://dx.doi.org/10.2172/952450.

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Seroussi, Eyal, and George Liu. Genome-Wide Association Study of Copy Number Variation and QTL for Economic Traits in Holstein Cattle. United States Department of Agriculture, September 2010. http://dx.doi.org/10.32747/2010.7593397.bard.

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Copy number variation (CNV) has been recently identified in human and other mammalian genomes and increasing awareness that CNV might be a major source for heritable variation in complex traits has emerged. Despite this, little has been published on CNVs in Holsteins. In order to fill this knowledge-gap, we proposed a genome-wide association study between quantitative trait loci (QTL) for economic traits and CNV in the Holstein cattle. The approved feasibility study was aimed at the genome-wide characterization of CNVs in Holstein cattle and at the demonstrating of their possible association with economic traits by performing the activities of preparation of DNA samples, Comparative Genomic Hybridization (CGH), initial association study between CNVs and production traits and characterization of CNVSNP associations. For both countries, 40 genomic DNA samples of bulls representing the extreme sub-populations for economically important traits were CGH analyzed using the same reference genome on a NimbleGen tiling array. We designed this array based on the latest build of the bovine genome (UMD3) with average probe spacing of 1150 bases (total number of probes was 2,166,672). Two CNV gene clusters, PLA2G2D on BTA2 and KIAA1683 on BTA7 revealed significant association with milk percentage and cow fertility, respectively, and were chosen for further characterization and verification in a larger sample using other methodologies including sequencing, tag SNPs and real time PCR (qPCR). Comparison between these four methods indicated that there is under estimation of the number of CNV loci in Holstein cattle and their complexity. The variation in sequence between different copies seemed to affect their functionality and thus the hybridization based methods were less informative than the methods that are based on sequencing. We thus conclude that large scale sequencing effort complemented by array CGH should be considered to better detect and characterize CNVs in order to effectively employ them in marker-assisted selection.

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Wu, Liyou, T. Y. Yi, Joy Van Nostrand, and Jizhong Zhou. Phylogenetic Analysis of Shewanella Strains by DNA Relatedness Derived from Whole Genome Microarray DNA-DNA Hybridization and Comparison with Other Methods. Office of Scientific and Technical Information (OSTI), May 2010. http://dx.doi.org/10.2172/986917.

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Ahlgren, Per, Tobias Jeppsson, Esa Stenberg, and Erik Berg. A bibliometric analysis of battery research with the BATTERY 2030+ roadmap as point of departure. Uppsala universitet, 2022. http://dx.doi.org/10.33063/diva-473454.

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In this bibliometric study, we analyze the six battery research subfields identified in the BATTERY 2030+ roadmap: Battery Interface Genome, Materials Acceleration Platform, Recyclability, Smart functionalities: Self-healing, Smart functionalities: Sensing, and Manufacturability. In addition, we analyze the entire research field related to BATTERY 2030+ as a whole, using two operationalizations. We (a) evaluate the European standing in the subfields/the BATTERY 2030+ field in comparison to the rest of the world, and (b) identify strongholds of the subfields/the BATTERY 2030+ field across Europe. For each subfield and the field as a whole, we used seed articles, i.e. articles listed in the BATTERY 2030+ roadmap or cited by such articles, in order to generate additional, similar articles located in an algorithmically obtained classification system. The output of the analysis is publication volumes, field normalized citation impact values with comparisons between country/country aggregates and between organizations, co-publishing networks between countries and organizations, and keyword co-occurrence networks. For the results related to (a), the performance of EU & associated (countries) is similar to China and the aggregate Japan-South Korea-Singapore and well below North America regarding citation impact and with respect to the field as a whole. Exceptions are, however, the subfields Battery Interface Genome and Recyclability. For the results related to (b), there is a large variability in the EU & associated organizations regarding volume in the different subfields. For citation impact, examples of high-performing EU & associated organizations are ETH Zurich and Max Planck Society for the Advancement of Science.

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Barash, Itamar, J. Mina Bissell, Alexander Faerman, and Moshe Shani. Modification of Milk Composition via Transgenesis: The Role of the Extracellular Matrix in Regulating Transgene Expression. United States Department of Agriculture, July 1995. http://dx.doi.org/10.32747/1995.7570558.bard.

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Altering milk composition via transgenesis depends on three main factors. (1) The availability of an efficient regulatory sequences for targeting transgene(s) to the mammary gland; (2) a reliable in vitro model to test the expression of transgenes prior to their introduction to the animal genome; and (3) better understanding of the major factors which determine the rate of gene expression and protein synthesis. The current studies provide the necessary means and knowledge to alter milk protein composition via transgenesis. The following specific goals were achieved: a: Identifying regulatory regions in the b-lactoglobulin (BLG) gene and the cross-talk between elements which enabled us to construct an efficient vector for the expression of desirable cDNA's in the mammary gland. b: The establishment of a sheep mammary cell line that serves as a model for the analysis of endogenous and exogenous milk protein synthesis in the mammary gland of livestock. c: An accurate comparison of the potency of the 5' regulatory sequences from the BLG and whey acidic protein (WAP) promoters in directing the expression of human serum albumin (HSA) to the mammary gland in vitro and in vivo. In this study we have also shown that sequences within the coding region may determine a specific pattern of expression for the transgene, distinct from that of the native milk protein genes. d: Characterizing the dominant role of ECM in transgene expression in mammary epithelial cells. e: Further characterization of the BCE-1 enhancer element in the promoter of the b-casein gene as a binding site for the c/EBP-b and Stat5. Identifying its interaction with chromatin and its up regulation by inhibitors of histone deacetylation. f: Identifying a mechanism of translational control as a mediator for the synergistic effect of insulin and prolactin on protein synthesis in the mammary gland.

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George M. Church. Genomic Sequence Comparisons, 1987-2003 Final Report. Office of Scientific and Technical Information (OSTI), July 2004. http://dx.doi.org/10.2172/827024.

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Timme, Ruth E., Jennifer V. Kuehl, Jeffrey L. Boore, and Robert K. Jansen. A Comparison of the First Two Sequenced Chloroplast Genomes in Asteraceae: Lettuce and Sunflower. Office of Scientific and Technical Information (OSTI), January 2006. http://dx.doi.org/10.2172/960402.

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Fromm, Hillel, Paul Michael Hasegawa, and Aaron Fait. Calcium-regulated Transcription Factors Mediating Carbon Metabolism in Response to Drought. United States Department of Agriculture, June 2013. http://dx.doi.org/10.32747/2013.7699847.bard.

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Original objectives: The long-term goal of the proposed research is to elucidate the transcription factors, genes and metabolic networks involved in carbon metabolism and partitioning in response to water deficit. The proposed research focuses on the GTLcalcium/calmodulinbindingTFs and the gene and metabolic networks modulated by these TFs in Arabidopsis thaliana. The specific objectives are as follows. Objective-1 (USA): Physiological analyses of GTL1 loss- and gain-of-function plants under water sufficient and drought stress conditions Objective 2 (USA / Israel-TAU): Characterizion of GTL target genes and bioinformatic analysis of data to eulcidate gene-network topology. Objective-3 (Israel-TAU): Regulation of GTLmediated transcription by Ca²⁺/calmodulin: mechanism and biological significance. Objective-4 (Israel-BGU): Metabolic networks and carbon partitioning in response to drought. Additional direction: In the course of the project we added another direction, which was reported in the 2nd annual report, to elucidate genes controlling drought avoidance. The TAU team has isolated a few unhydrotropic (hyd) mutants and are in the process of mapping these mutations (of hyd13 and hyd15; see last year's report for a description of these mutants under salt stress) in the Arabidopsis genome by map-based cloning and deep sequencing. For this purpose, each hyd mutant was crossed with a wild type plant of the Landsberg ecotype, and at the F2 stage, 500-700 seedlings showing the unhydrotropic phenotype were collected separately and pooled DNA samples were subkected to the Illumina deep sequencing technology. Bioinformatics were used to identify the exact genomic positions of the mutations (based on a comparison of the genomic sequences of the two Arabidopsis thaliana ecotypes (Columbia and Landsberg). Background: To feed the 9 billion people or more, expected to live on Earth by the mid 21st century, the production of high-quality food must increase substantially. Based on a 2009 Declaration of the World Summit on Food Security, a target of 70% more global food production by the year 2050 was marked, an unprecedented food-production growth rate. Importantly, due to the larger areas of low-yielding land globally, low-yielding environments offer the greatest opportunity for substantial increases in global food production. Nowadays, 70% of the global available water is used by agriculture, and 40% of the world food is produced from irrigated soils. Therefore, much needs to be done towards improving the efficiency of water use by plants, accompanied by increased crop yield production under water-limiting conditions. Major conclusions, solutions and achievements: We established that AtGTL1 (Arabidopsis thaliana GT-2 LIKE1) is a focal determinant in water deficit (drought) signaling and tolerance, and water use efficiency (WUE). The GTL1 transcription factor is an upstream regulator of stomatal development as a transrepressor of AtSDD1, which encodes a subtilisin protease that activates a MAP kinase pathway that negatively regulates stomatal lineage and density. GTL1 binds to the core GT3 cis-element in the SDD1 promoter and transrepresses its expression under water-sufficient conditions. GTL1 loss-of-function mutants have reduced stomatal number and transpiration, and enhanced drought tolerance and WUE. In this case, higher WUE under water sufficient conditions occurs without reduction in absolute biomass accumulation or carbon assimilation, indicating that gtl1-mediated effects on stomatal conductance and transpiration do not substantially affect CO₂ uptake. These results are proof-of-concept that fine-tuned regulation of stomatal density can result in drought tolerance and higher WUE with maintenance of yield stability. Implications: Accomplishments during the IS-4243-09R project provide unique tools for continued discovery research to enhance plant drought tolerance and WUE.

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Palmer, Guy, Varda Shkap, Wendy Brown, and Thea Molad. Control of bovine anaplasmosis: cytokine enhancement of vaccine efficacy. United States Department of Agriculture, March 2007. http://dx.doi.org/10.32747/2007.7695879.bard.

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Anaplasmosis an arthropod-born disease of cattle caused by the rickettsia Anaplasma marginale and is an impediment to efficient production of healthy livestock in both Israel and the United States. Currently the only effective vaccines are derived from the blood of infected cattle. The risk of widespread transmission of both known and newly emergent pathogens has prevented licensure of live blood-based vaccines in the U.S. and is a major concern for their continued use in Israel. Consequently development of a safe, effective vaccine is a high priority. In this collaborative project we focused on two approaches to vaccine development. The first focused o n improving antigen delivery to livestock and specifically examined how DNA vaccines could be improved to enhance priming and expansion of the immune response. This research resulted in development and testing of two novel vaccine delivery systems--one that targeted antigen spread among dendritic cells (the key cell in priming immune responses and a follow-on construct that also specifically targeted antigen to the endosomal-lysosomal compartment the processing organelle within the dendritic cell that directs vaccine antigen to the MHC class ll-CD4* T cell priming pathway). The optimized construct targeting vaccine antigen to the dendritic cell MHC class II pathway was tested for ability to prime A. marginale specific immune responses in outbred cattle. The results demonstrated both statistically significant effects of priming with a single immunization, continued expansion of the primary immune response including development of high affinity lgG antibodies and rapid recall of the memory response following antigen challenge. This portion of the study represented a significant advance in vaccine delivery for livestock. Importantly the impact of these studies is not limited to A. marginale a s the targeting motifs are optimized for cattle and can be adapted to other cattle vaccinations by inserting a relevant pathogen-specific antigen. The second approach (which represented an addition to the project for which approval was requested as part of the first annual report) was a comparative approach between A . marginale and the Israel A . centrale vaccines train. This addition was requested as studies on Major Surface Protein( MSP)- 2 have shown that this antigen is highly antigenically variable and presented solely as a "static vaccine" antigen does not give cross-strain immunity. In contrast A. . centrale is an effective vaccine which Kimron Veterinary institute has used in the field in Israel for over 50 years. Taking advantage of this expertise, a broad comparison of wild type A. marginale and vaccine strain was initiated. These studies revealed three primary findings: i) use of the vaccine is associated with superinfection, but absence of clinical disease upon superinfection with A. marginale; ii) the A. centrale vaccine strain is not only less virulent but transmission in competent in Dermacentor spp. ticks; and iii) some but not all MSPs are conserved in basic orthologous structure but there are significant polymorphisms among the strains. These studies clearly indicated that there are statistically significant differences in biology (virulence and transmission) and provide a clear path for mapping of biology with the genomes. Based on these findings, we initiated complete genome sequencing of the Israel vaccine strain (although not currently funded by BARD) and plant to proceed with a comparative genomics approach using already sequenced wild-type A. marginale. These findings and ongoing collaborative research tie together filed vaccine experience with new genomic data, providing a new approach to vaccine development against a complex pathogen.

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Dillman III, James F., and Christopher S. Phillips. Comparison of Non-Human Primate and Human Whole Blood Tissue Gene Expression Profiles. Fort Belvoir, VA: Defense Technical Information Center, March 2005. http://dx.doi.org/10.21236/ada443193.

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