Daojun Yuan, Ph.D. - Related publications

2015-2018 Plant and Wildlife Sciences Brigham Young University, Provo, UT, United States 
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Shirasawa K, Harada D, Hirakawa H, Isobe S, Kole C. Chromosome-level genome assemblies of over 100 plant species. Breeding Science. 71: 117-124. PMID 34377059 DOI: JST.JSTAGE/jsbbs/20146   
2021 Li S, Zhao G, Han H, Li Y, Li J, Wang J, Cao G, Li X. Genome collinearity analysis illuminates the evolution of donkey chromosome 1 and horse chromosome 5 in perissodactyls: A comparative study. Bmc Genomics. 22: 665. PMID 34521340 DOI: 10.1186/s12864-021-07984-6   
2021 Sharon BM, Hulyalkar NV, Nguyen VH, Zimmern PE, Palmer KL, De Nisco NJ. Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies. Journal of Visualized Experiments : Jove. PMID 34487123 DOI: 10.3791/62872   
2021 Woodhouse MR, Cannon EK, Portwood JL, Harper LC, Gardiner JM, Schaeffer ML, Andorf CM. A pan-genomic approach to genome databases using maize as a model system. Bmc Plant Biology. 21: 385. PMID 34416864 DOI: 10.1186/s12870-021-03173-5   
2021 Vega-Estévez S, Armitage A, Bates HJ, Harrison RJ, Buscaino A. The Genome of the CTG(Ser1) Yeast Is Plastic. Mbio. e0187121. PMID 34488452 DOI: 10.1128/mBio.01871-21   
2021 Kim MS, Lee T, Baek J, Kim JH, Kim C, Jeong SC. Genome assembly of the popular Korean soybean cultivar Hwangkeum. G3 (Bethesda, Md.). 11. PMID 34568925 DOI: 10.1093/g3journal/jkab272   
2021 Saha S, Cooksey AM, Childers AK, Poelchau MF, McCarthy FM. Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes. Insects. 12. PMID 34442314 DOI: 10.3390/insects12080748   
2021 Alabi N, Wu Y, Bossdorf O, Rieseberg LH, Colautti RI. Genome Report: A draft genome of Alliaria petiolata (garlic mustard) as a model system for invasion genetics. G3 (Bethesda, Md.). PMID 34599816 DOI: 10.1093/g3journal/jkab339   
2021 Zhang F, Wang N, Cheng G, Shu X, Wang T, Zhuang W, Lu R, Wang Z. Comparative Chloroplast Genomes of Four Species (Amaryllidaceae) Provides New Insight into Interspecific Relationship and Phylogeny. Biology. 10. PMID 34439948 DOI: 10.3390/biology10080715   
2021 Yuan XL, Zhang CS, Kong FY, Zhang ZF, Wang FL. Genome Analysis of JM01 Provides Insights into Its Pathogenicity Mechanisms. Plants (Basel, Switzerland). 10. PMID 34451665 DOI: 10.3390/plants10081620   
2021 Shan Y, Pei X, Yong S, Li J, Qin Q, Zeng S, Yu J. Analysis of the complete chloroplast genomes of and (Lamiaceae). Mitochondrial Dna. Part B, Resources. 6: 2672-2680. PMID 34435116 DOI: 10.1080/23802359.2021.1920491   
2021 Kang L, Michalak P, Hallerman E, Moncrief ND. A Draft Genome Assembly for the Eastern Fox Squirrel, Sciurus niger. G3 (Bethesda, Md.). PMID 34550334 DOI: 10.1093/g3journal/jkab315   
2021 Grover CE, Yuan D, Arick MA, Miller ER, Hu G, Peterson DG, Wendel JF, Udall JA. The Gossypium anomalum genome as a resource for cotton improvement and evolutionary analysis of hybrid incompatibility. G3 (Bethesda, Md.). PMID 34549783 DOI: 10.1093/g3journal/jkab319   
2021 Chen Z, Shen M, Mao C, Wang C, Yuan P, Wang T, Sun D. A Type I Restriction Modification System Influences Genomic Evolution Driven by Horizontal Gene Transfer in . Frontiers in Microbiology. 12: 709571. PMID 34413842 DOI: 10.3389/fmicb.2021.709571   
2021 Driguez P, Bougouffa S, Carty K, Putra A, Jabbari K, Reddy M, Soppe R, Cheung MS, Fukasawa Y, Ermini L. LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology. Genome Biology. 22: 256. PMID 34479618 DOI: 10.1186/s13059-021-02475-z   
2021 Ren F, Wang L, Zhuo W, Lu S, Zhu X, Liu C, Yang M. First complete chloroplast genome of the rare medicinal plant . Mitochondrial Dna. Part B, Resources. 6: 2993-2994. PMID 34568558 DOI: 10.1080/23802359.2021.1975507   
2021 Wijayasekara D, Ali A. Evolutionary study of maize dwarf mosaic virus using nearly complete genome sequences acquired by next-generation sequencing. Scientific Reports. 11: 18786. PMID 34552152 DOI: 10.1038/s41598-021-98299-9   
2021 Ulaszewski B, Meger J, Mishra B, Thines M, Burczyk J. Complete Chloroplast Genomes of L. Reveal Sequence Conservation in the Inverted Repeat and the Presence of Allelic Variation in NUPTs. Genes. 12. PMID 34573338 DOI: 10.3390/genes12091357   
2021 Galvez LC, Koh RBL, Barbosa CFC, Asunto JC, Catalla JL, Atienza RG, Costales KT, Aquino VM, Zhang D. Sequencing and de Novo Assembly of Abaca ( Née) var. Abuab Genome. Genes. 12. PMID 34440376 DOI: 10.3390/genes12081202   
2021 Li Q, Tian S, Yan B, Liu CM, Lam TW, Li R, Luo R. Building a Chinese pan-genome of 486 individuals. Communications Biology. 4: 1016. PMID 34462542 DOI: 10.1038/s42003-021-02556-6   
2021 Istace B, Belser C, Falentin C, Labadie K, Boideau F, Deniot G, Maillet L, Cruaud C, Bertrand L, Chèvre AM, Wincker P, Rousseau-Gueutin M, Aury JM. Sequencing and Chromosome-Scale Assembly of Plant Genomes, as a Use Case. Biology. 10. PMID 34439964 DOI: 10.3390/biology10080732   
2021 Tian C, Li X, Wu Z, Li Z, Hou X, Li FY. Characterization and Comparative Analysis of Complete Chloroplast Genomes of Three Species From the Genus (Leguminosae). Frontiers in Genetics. 12: 705482. PMID 34422006 DOI: 10.3389/fgene.2021.705482   
2021 Yamaguchi K, Kadota M, Nishimura O, Ohishi Y, Naito Y, Kuraku S. Technical considerations in Hi-C scaffolding and evaluation of chromosome-scale genome assemblies. Molecular Ecology. PMID 34432923 DOI: 10.1111/mec.16146   
2021 Al-Qurainy F, Gaafar AZ, Khan S, Nadeem M, Alshameri AM, Tarroum M, Alansi S, Almarri NB, Alfarraj NS. Estimation of Genome Size in the Endemic Species and the Locally Rare Species Using comparative Analyses of Flow Cytometry and K-Mer Approaches. Plants (Basel, Switzerland). 10. PMID 34371565 DOI: 10.3390/plants10071362   
2021 Luzuriaga-Aveiga VE, Ugarte M, Weir JT. Distinguishing genomic homogenization from parapatric speciation in an elevationally replacing pair of Ramphocelus tanagers. Molecular Ecology. PMID 34403554 DOI: 10.1111/mec.16128   
2021 Zeng Q, Liu J, Wang C, Wang H, Zhang L, Hu J, Bao L, Wang S. High-quality reannotation of the king scallop genome reveals no 'gene-rich' feature and evolution of toxin resistance. Computational and Structural Biotechnology Journal. 19: 4954-4960. PMID 34527199 DOI: 10.1016/j.csbj.2021.08.038   
2021 Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Molecular Biology and Evolution. PMID 34320186 DOI: 10.1093/molbev/msab199   
2021 Zang F, Ma Y, Tu X, Huang P, Wu Q, Li Z, Liu T, Lin F, Pei S, Zang D, Zhang X, Zheng Y, Yu Y. A high-quality chromosome-level genome of wild Rosa rugosa. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. PMID 34499118 DOI: 10.1093/dnares/dsab017   
2021 Oggenfuss U, Badet T, Wicker T, Hartmann FE, Singh NK, Abraham L, Karisto P, Vonlanthen T, Mundt C, McDonald BA, Croll D. A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen. Elife. 10. PMID 34528512 DOI: 10.7554/eLife.69249   
2021 Wold J, Koepfli KP, Galla SJ, Eccles D, Hogg CJ, Le Lec MF, Guhlin J, Santure AW, Steeves TE. Expanding the conservation genomics toolbox: incorporating structural variants to enhance genomic studies for species of conservation concern. Molecular Ecology. PMID 34424587 DOI: 10.1111/mec.16141   
2021 Zhang L, Wang S, Su C, Harris AJ, Zhao L, Su N, Wang JR, Duan L, Chang ZY. Comparative Chloroplast Genomics and Phylogenetic Analysis of (Zygophyllaceae) of China. Frontiers in Plant Science. 12: 723622. PMID 34630471 DOI: 10.3389/fpls.2021.723622   
2021 Lupande-Mwenebitu D, Khedher MB, Khabthani S, Rym L, Phoba MF, Nabti LZ, Lunguya-Metila O, Pantel A, Lavigne JP, Rolain JM, Diene SM. First Genome Description of Isolate Bearing NDM-1 from Blood Culture. Microorganisms. 9. PMID 34442831 DOI: 10.3390/microorganisms9081751   
2021 Patino LH, Castillo-Castañeda A, Muñoz M, Muskus C, Rivero-Rodríguez M, Pérez-Doria A, Bejarano EE, Ramírez JD. Revisiting the heterogeneous global genomic population structure of . Microbial Genomics. 7. PMID 34491157 DOI: 10.1099/mgen.0.000640   
2021 Sun N, Pei S, He L, Yin C, He RL, Yau SS. Geometric construction of viral genome space and its applications. Computational and Structural Biotechnology Journal. 19: 4226-4234. PMID 34429843 DOI: 10.1016/j.csbj.2021.07.028   
2021 Hutter CR, Cobb KA, Portik DM, Travers SL, Wood PL, Brown RM. FrogCap: A modular sequence capture probe-set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales. Molecular Ecology Resources. PMID 34569723 DOI: 10.1111/1755-0998.13517   
2021 Jiang M, Zhu Y, Wu Q, Zhang H. Complete chloroplast genome of a rare and endangered plant species : genomic features and phylogenetic relationship within Orchidaceae. Mitochondrial Dna. Part B, Resources. 6: 2872-2879. PMID 34532575 DOI: 10.1080/23802359.2021.1972049   
2021 Trujillo-Montenegro JH, Rodríguez Cubillos MJ, Loaiza CD, Quintero M, Espitia-Navarro HF, Salazar Villareal FA, Viveros Valens CA, González Barrios AF, De Vega J, Duitama J, Riascos JJ. Unraveling the Genome of a High Yielding Colombian Sugarcane Hybrid. Frontiers in Plant Science. 12: 694859. PMID 34484261 DOI: 10.3389/fpls.2021.694859   
2021 Fan ZF, Yu DY, Ma CL. The complete chloroplast genome sequence of Rolfe, a vulnerable wild moth orchid species (Orchidaceae). Mitochondrial Dna. Part B, Resources. 6: 2903-2905. PMID 34532582 DOI: 10.1080/23802359.2021.1923420   
2021 Padhi EM, Ng JK, Mehinovic E, Sams EI, Turner TN. ACES: Analysis of Conservation with an Extensive list of Species. Bioinformatics (Oxford, England). PMID 34601580 DOI: 10.1093/bioinformatics/btab684   
2021 Maroilley T, Li X, Oldach M, Jean F, Stasiuk SJ, Tarailo-Graovac M. Deciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing. Scientific Reports. 11: 18258. PMID 34521941 DOI: 10.1038/s41598-021-97764-9   
2021 Li Y, Liu H, Zou J. Complete chloroplast genome of : a species endemic to Guizhou, China. Mitochondrial Dna. Part B, Resources. 6: 2596-2598. PMID 34395889 DOI: 10.1080/23802359.2021.1961625   
2021 Yousaf A, Liu J, Ye S, Chen H. Current Progress in Evolutionary Comparative Genomics of Great Apes. Frontiers in Genetics. 12: 657468. PMID 34456962 DOI: 10.3389/fgene.2021.657468   
2021 Quan W, Liu B, Wang Y. Fast and SNP-aware short read alignment with SALT. Bmc Bioinformatics. 22: 172. PMID 34433415 DOI: 10.1186/s12859-021-04088-6   
2021 Paterson GK. Genomic epidemiology of the opportunistic pathogen from companion dogs. Journal of Medical Microbiology. 70. PMID 34431760 DOI: 10.1099/jmm.0.001407   
2021 Lee JH, Siddique MI, Kwon JK, Kang BC. Comparative Genomic Analysis Reveals Genetic Variation and Adaptive Evolution in the Pathogenicity-Related Genes of . Frontiers in Microbiology. 12: 694136. PMID 34484141 DOI: 10.3389/fmicb.2021.694136   
2021 Wang Y, Zhang R, Wang M, Zhang L, Shi CM, Li J, Fan F, Geng S, Liu X, Yang D. The first chromosome-level genome assembly of a green lacewing Chrysopa pallens and its implication for biological control. Molecular Ecology Resources. PMID 34549894 DOI: 10.1111/1755-0998.13503   
2021 Van Dam MH, Cabras AA, Henderson JB, Rominger AJ, Pérez Estrada C, Omer AD, Dudchenko O, Lieberman Aiden E, Lam AW. The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution. Plos Genetics. 17: e1009745. PMID 34460814 DOI: 10.1371/journal.pgen.1009745   
2021 Jiang X, Xu Z, Zhang T, Li Y, Li W, Tan H. Whole-Genome-Based Geographic Surveillance: A Visualized and Expandable Webtool. Frontiers in Microbiology. 12: 687259. PMID 34408729 DOI: 10.3389/fmicb.2021.687259   
2021 Hong Z, Liao X, Ye Y, Zhang N, Yang Z, Zhu W, Gao W, Sharbrough J, Tembrock LR, Xu D, Wu Z. A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers. Bmc Genomics. 22: 672. PMID 34536995 DOI: 10.1186/s12864-021-07967-7   
2021 Richardson JE, Baldarelli RM, Bult CJ. Multiple genome viewer (MGV): a new tool for visualization and comparison of multiple annotated genomes. Mammalian Genome : Official Journal of the International Mammalian Genome Society. PMID 34448927 DOI: 10.1007/s00335-021-09904-1