Linyang Ju - Related publications

University of Pennsylvania, Philadelphia, PA, United States 
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50 most relevant papers in past 60 days:
Year Citation  Score
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 Wee SK, Yap EPH. GALAXY Workflow for Bacterial Next-Generation Sequencing De Novo Assembly and Annotation. Current Protocols. 1: e242. PMID 34491622 DOI: 10.1002/cpz1.242   
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 Chen E, Chu J, Zhang J, Warren R, Birol I. GapPredict A Language Model for Resolving Gaps in Draft Genome Assemblies. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 34478378 DOI: 10.1109/TCBB.2021.3109557   
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 Wang J, Chen K, Ren Q, Zhang Y, Liu J, Wang G, Liu A, Li Y, Liu G, Luo J, Miao W, Xiong J, Yin H, Guan G. Systematic Comparison of the Performances of Genome Assemblers for Oxford Nanopore Technology Reads From Piroplasm. Frontiers in Cellular and Infection Microbiology. 11: 696669. PMID 34485177 DOI: 10.3389/fcimb.2021.696669   
2021 Liu YY, Chen BH, Chen CC, Chiou CS. Assessment of metrics in next-generation sequencing experiments for use in core-genome multilocus sequence type. Peerj. 9: e11842. PMID 34466283 DOI: 10.7717/peerj.11842   
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 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 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 Ekim B, Berger B, Chikhi R. Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer. Cell Systems. PMID 34525345 DOI: 10.1016/j.cels.2021.08.009   
2021 Ma X, Olsen JL, Reusch TBH, Procaccini G, Kudrna D, Williams M, Grimwood J, Rajasekar S, Jenkins J, Schmutz J, Van de Peer Y. Improved chromosome-level genome assembly and annotation of the seagrass, (eelgrass). F1000research. 10: 289. PMID 34621505 DOI: 10.12688/f1000research.38156.1   
2021 D'Huys L, Vitale R, Ruppeka-Rupeika E, Goyvaerts V, Ruckebusch C, Hofkens J. Assessing the Resolution of Methyltransferase-Mediated DNA Optical Mapping. Acs Omega. 6: 21276-21283. PMID 34471732 DOI: 10.1021/acsomega.1c01381   
2021 Hahn EE, Alexander MR, Grealy A, Stiller J, Gardiner DM, Holleley CE. Unlocking inaccessible historical genomes preserved in formalin. Molecular Ecology Resources. PMID 34549888 DOI: 10.1111/1755-0998.13505   
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 Guerrini MM, Oguchi A, Suzuki A, Murakawa Y. Cap analysis of gene expression (CAGE) and noncoding regulatory elements. Seminars in Immunopathology. PMID 34468849 DOI: 10.1007/s00281-021-00886-5   
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 Lee G, Kim MJ, Shin JH. Data on complete genome sequence and annotation of LMG 24727. Data in Brief. 38: 107271. PMID 34430681 DOI: 10.1016/j.dib.2021.107271   
2021 Deng A, Sun Z, Wang T, Cui D, Li L, Liu S, Huang F, Wen T. Simultaneous Multiplex Genome Engineering Accelerated Natural Transformation in . Frontiers in Microbiology. 12: 714449. PMID 34484154 DOI: 10.3389/fmicb.2021.714449   
2021 Umarov R, Li Y, Arakawa T, Takizawa S, Gao X, Arner E. ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation. Plos Computational Biology. 17: e1009376. PMID 34491989 DOI: 10.1371/journal.pcbi.1009376   
2021 Zhuo Z, Rong W, Li H, Li Y, Luo X, Liu Y, Tang X, Zhang L, Su F, Cui H, Xiao F. Long-read sequencing reveals the structural complexity of genomic integration of HBV DNA in hepatocellular carcinoma. Npj Genomic Medicine. 6: 84. PMID 34642322 DOI: 10.1038/s41525-021-00245-1   
2021 Bohálová N, Mergny JL, Brázda V. Novel G-quadruplex prone sequences emerge in the complete assembly of the human X chromosome. Biochimie. PMID 34508825 DOI: 10.1016/j.biochi.2021.09.004   
2021 Jaworski E, Langsjoen RM, Mitchell B, Judy B, Newman P, Plante JA, Plante KS, Miller AL, Zhou Y, Swetnam D, Sotcheff S, Morris V, Saada N, Machado RR, McConnell A, et al. Tiled-ClickSeq for targeted sequencing of complete coronavirus genomes with simultaneous capture of RNA recombination and minority variants. Elife. 10. PMID 34581669 DOI: 10.7554/eLife.68479   
2021 Huang N, Nie F, Ni P, Gao X, Luo F, Wang J. BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer. Briefings in Bioinformatics. PMID 34619757 DOI: 10.1093/bib/bbab405   
2021 Liu K, Gao Y, Li ZH, Liu M, Wang FQ, Wei DZ. CRISPR-Cas12a assisted precise genome editing of Mycolicibacterium neoaurum. New Biotechnology. PMID 34653700 DOI: 10.1016/j.nbt.2021.10.003   
2021 Tikariha H, Pavagadhi S, Mayalagu S, Poh MCH, Swarup S. Hybrid Genome Assembly for Predicting Functional Potential of a Novel Strain as Plant Biomass Valorisation Agent. Indian Journal of Microbiology. 61: 283-290. PMID 34294994 DOI: 10.1007/s12088-021-00935-5   
2021 Liu H, Li J, Lin Y, Bo X, Song H, Li K, Li P, Ni M. Assessment of two-pool multiplex long-amplicon nanopore sequencing of SARS-CoV-2. Journal of Medical Virology. PMID 34524690 DOI: 10.1002/jmv.27336   
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 Seah BKB, Swart EC. BleTIES: Annotation of natural genome editing in ciliates using long read sequencing. Bioinformatics (Oxford, England). PMID 34487139 DOI: 10.1093/bioinformatics/btab613   
2021 Dorado G, Gálvez S, Rosales TE, Vásquez VF, Hernández P. Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing - Review. Biomolecules. 11. PMID 34439777 DOI: 10.3390/biom11081111   
2021 Zhang X, Gu S, Zheng X, Peng S, Li Y, Lin Y, Liang S. A Novel and Efficient Genome Editing Tool Assisted by CRISPR-Cas12a/Cpf1 for . Acs Synthetic Biology. PMID 34644057 DOI: 10.1021/acssynbio.1c00172   
2021 Heckel DG. Perspectives on gene copy number variation and pesticide resistance. Pest Management Science. PMID 34480789 DOI: 10.1002/ps.6631   
2021 Foox J, Tighe SW, Nicolet CM, Zook JM, Byrska-Bishop M, Clarke WE, Khayat MM, Mahmoud M, Laaguiby PK, Herbert ZT, Warner D, Grills GS, Jen J, Levy S, Xiang J, et al. Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study. Nature Biotechnology. 39: 1129-1140. PMID 34504351 DOI: 10.1038/s41587-021-01049-5   
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 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 Sajib AM, Agarwal P, Patton DJ, Nance RL, Stahr NA, Kretzschmar WP, Sandey M, Smith BF. In vitro functional genetic modification of canine adenovirus type 2 genome by CRISPR/Cas9. Laboratory Investigation; a Journal of Technical Methods and Pathology. PMID 34417549 DOI: 10.1038/s41374-021-00654-x   
2021 Xie Z, Dang J, Wen G, Wang H, Guo Q, Liang G. [Advances in identification methods of alien genomic components in plants]. Sheng Wu Gong Cheng Xue Bao = Chinese Journal of Biotechnology. 37: 2703-2718. PMID 34472290 DOI: 10.13345/j.cjb.200702   
2021 Ettinger CL, Byrne FJ, Collin MA, Carter-House D, Walling LL, Atkinson PW, Redak RA, Stajich JE. Improved draft reference genome for the Glassy-winged Sharpshooter (Homalodisca vitripennis), a vector for Pierce's disease. G3 (Bethesda, Md.). 11. PMID 34568917 DOI: 10.1093/g3journal/jkab255   
2021 Lewis S, Nash A, Li Q, Ahn TH. Comparison of 16S and whole genome dog microbiomes using machine learning. Biodata Mining. 14: 41. PMID 34419136 DOI: 10.1186/s13040-021-00270-x   
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 Udaondo Z, Sittikankaew K, Uengwetwanit T, Wongsurawat T, Sonthirod C, Jenjaroenpun P, Pootakham W, Karoonuthaisiri N, Nookaew I. Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of . Life (Basel, Switzerland). 11. PMID 34440606 DOI: 10.3390/life11080862   
2021 Wright BW, Molloy MP, Jaschke PR. Overlapping genes in natural and engineered genomes. Nature Reviews. Genetics. PMID 34611352 DOI: 10.1038/s41576-021-00417-w   
2021 Kanwar N, Blanco C, Chen IA, Seelig B. PacBio sequencing output increased through uniform and directional fivefold concatenation. Scientific Reports. 11: 18065. PMID 34508117 DOI: 10.1038/s41598-021-96829-z   
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 Moolhuijzen P, See PT, Moffat CS. The first genome assembly of fungal pathogen Pyrenophora tritici-repentis race 1 isolate using Oxford Nanopore MinION sequencing. Bmc Research Notes. 14: 334. PMID 34454585 DOI: 10.1186/s13104-021-05751-0   
2021 Christiansen H, Heindler FM, Hellemans B, Jossart Q, Pasotti F, Robert H, Verheye M, Danis B, Kochzius M, Leliaert F, Moreau C, Patel T, Van de Putte AP, Vanreusel A, Volckaert FAM, et al. Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing. Bmc Genomics. 22: 625. PMID 34418978 DOI: 10.1186/s12864-021-07917-3   
2021 Liu Y, Huang L, Hu H, Cai M, Liang X, Li X, Zhang Z, Xie Y, Xiao C, Chen S, Chen D, Yong T, Pan H, Gao X, Wu Q. Whole-genome assembly of Ganoderma leucocontextum (Ganodermataceae, Fungi) discovered from the Tibetan Plateau of China. G3 (Bethesda, Md.). PMID 34586388 DOI: 10.1093/g3journal/jkab337   
2021 Seher TD, Nguyen N, Ramos D, Bapat P, Nobile CJ, Sindi SS, Hernday AD. AddTag, a two-step approach with supporting software package that facilitates CRISPR/Cas-mediated precision genome editing. G3 (Bethesda, Md.). 11. PMID 34544122 DOI: 10.1093/g3journal/jkab216   
2021 Zhou XJ, Li JT, Wang HL, Han JW, Zhang K, Dong SW, Zhang YZ, Ya HY, Cheng YW, Sun SS. The chromosome-scale genome assembly, annotation and evolution of Rhododendron henanense subsp. lingbaoense. Molecular Ecology Resources. PMID 34652864 DOI: 10.1111/1755-0998.13529   
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