Daryl J. Thomas, Ph.D. - Related publications

Affiliations: 
University of California, Santa Cruz, Santa Cruz, CA, United States 
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Mun S, Kim S, Lee W, Kang K, Meyer TJ, Han BG, Han K, Kim HS. A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome. Experimental & Molecular Medicine. PMID 33833373 DOI: 10.1038/s12276-021-00586-y   
2021 Zhao X, Collins RL, Lee WP, Weber AM, Jun Y, Zhu Q, Weisburd B, Huang Y, Audano PA, Wang H, Walker M, Lowther C, Fu J, , Gerstein MB, et al. Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies. American Journal of Human Genetics. PMID 33789087 DOI: 10.1016/j.ajhg.2021.03.014   
2021 Wahlster L, Verboon JM, Ludwig LS, Black SC, Luo W, Garg K, Voit RA, Collins RL, Garimella K, Costello M, Chao KR, Goodrich JK, DiTroia SP, O'Donnell-Luria A, Talkowski ME, et al. Familial thrombocytopenia due to a complex structural variant resulting in a WAC-ANKRD26 fusion transcript. The Journal of Experimental Medicine. 218. PMID 33857290 DOI: 10.1084/jem.20210444   
2021 Jeffet J, Margalit S, Michaeli Y, Ebenstein Y. Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale. Essays in Biochemistry. PMID 33739394 DOI: 10.1042/EBC20200021   
2021 Pereira J. GCsnap: interactive snapshots for the comparison of protein-coding genomic contexts. Journal of Molecular Biology. 166943. PMID 33737026 DOI: 10.1016/j.jmb.2021.166943   
2021 Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 592: 737-746. PMID 33911273 DOI: 10.1038/s41586-021-03451-0   
2021 Lei L, Goltsman E, Goodstein D, Wu GA, Rokhsar DS, Vogel JP. Plant Pan-Genomics Comes of Age. Annual Review of Plant Biology. PMID 33848428 DOI: 10.1146/annurev-arplant-080720-105454   
2021 Kwon SB, Ernst J. Learning a genome-wide score of human-mouse conservation at the functional genomics level. Nature Communications. 12: 2495. PMID 33941776 DOI: 10.1038/s41467-021-22653-8   
2021 Zhou J, Zhang S, Wang J, Shen H, Ai B, Gao W, Zhang C, Fei Q, Yuan D, Wu Z, Tembrock LR, Li S, Gu C, Liao X. Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution. Scientific Reports. 11: 9471. PMID 33947883 DOI: 10.1038/s41598-021-88160-4   
2021 Modak TH, Literman R, Puritz JB, Johnson KM, Roberts EM, Proestou D, Guo X, Gomez-Chiarri M, Schwartz RS. Extensive genome-wide duplications in the eastern oyster (). Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 376: 20200164. PMID 33813893 DOI: 10.1098/rstb.2020.0164   
2021 Sommer MJ, Salzberg SL. Balrog: A universal protein model for prokaryotic gene prediction. Plos Computational Biology. 17: e1008727. PMID 33635857 DOI: 10.1371/journal.pcbi.1008727   
2021 Marchi N, Schlichta F, Excoffier L. Demographic inference. Current Biology : Cb. 31: R276-R279. PMID 33756135 DOI: 10.1016/j.cub.2021.01.053   
2021 Lopes M, Louzada S, Gama-Carvalho M, Chaves R. Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time. International Journal of Molecular Sciences. 22. PMID 33946766 DOI: 10.3390/ijms22094707   
2021 Prokopenko D, Morgan SL, Mullin K, Hofmann O, Chapman B, Kirchner R, , Amberkar S, Wohlers I, Lange C, Hide W, Bertram L, Tanzi RE. Whole-genome sequencing reveals new Alzheimer's disease-associated rare variants in loci related to synaptic function and neuronal development. Alzheimer's & Dementia : the Journal of the Alzheimer's Association. PMID 33797837 DOI: 10.1002/alz.12319   
2021 Misztal I, Aguilar I, Lourenco D, Ma L, Steibel J, Toro M. Emerging issues in genomic selection. Journal of Animal Science. PMID 33773494 DOI: 10.1093/jas/skab092   
2021 Jinyu L, Shan Y, Yujun C, Tao W, Yue T. Research progress of bacterial minimal genome. Yi Chuan = Hereditas. 43: 142-159. PMID 33724217 DOI: 10.16288/j.yczz.20-301   
2021 Weng YM, Francoeur CB, Currie CR, Kavanaugh DH, Schoville SD. A high-quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation. Molecular Ecology Resources. PMID 33938156 DOI: 10.1111/1755-0998.13409   
2021 Vitsios D, Dhindsa RS, Middleton L, Gussow AB, Petrovski S. Prioritizing non-coding regions based on human genomic constraint and sequence context with deep learning. Nature Communications. 12: 1504. PMID 33686085 DOI: 10.1038/s41467-021-21790-4   
2021 Katsura Y, Ikemura T, Kajitani R, Toyoda A, Itoh T, Ogata M, Miura I, Wada K, Wada Y, Satta Y. Comparative genomics of using unsupervised AI reveals a high CG frequency. Life Science Alliance. 4. PMID 33712508 DOI: 10.26508/lsa.202000905   
2021 Liu L, Chen R, Fugina CJ, Siegel B, Jackson D. High-Throughput and Low-Cost Genotyping Method for Plant Genome Editing. Current Protocols. 1: e100. PMID 33826801 DOI: 10.1002/cpz1.100   
2021 Sun J, Li Y, Ci X, Li X, Wang D, Cai N, Xu Y. The complete chloroplast genome of . Mitochondrial Dna. Part B, Resources. 6: 745-747. PMID 33763566 DOI: 10.1080/23802359.2020.1869606   
2021 Zou Y, Zhu Y, Li Y, Wu FX, Wang J. Parallel computing for genome sequence processing. Briefings in Bioinformatics. PMID 33822883 DOI: 10.1093/bib/bbab070   
2021 Zhu X, Wang J, Sun B, Ren C, Yang T, Ding J. An efficient ensemble method for missing value imputation in microarray gene expression data. Bmc Bioinformatics. 22: 188. PMID 33849444 DOI: 10.1186/s12859-021-04109-4   
2021 Wang D, Zheng Z, Li Y, Hu H, Wang Z, Du X, Zhang S, Zhu M, Dong L, Ren G, Yang Y. Which factors contribute most to genome size variation within angiosperms? Ecology and Evolution. 11: 2660-2668. PMID 33767827 DOI: 10.1002/ece3.7222   
2021 Hills M, Falconer E, O'Neill K, Sanders AD, Howe K, Guryev V, Lansdorp PM. Construction of Whole Genomes from Scaffolds Using Single Cell Strand-Seq Data. International Journal of Molecular Sciences. 22. PMID 33807210 DOI: 10.3390/ijms22073617   
2021 Hoffmann AA, Weeks AR, Sgrò CM. Opportunities and challenges in assessing climate change vulnerability through genomics. Cell. 184: 1420-1425. PMID 33740448 DOI: 10.1016/j.cell.2021.02.006   
2021 Ciobanu D, Clum A, Ahrendt S, Andreopoulos WB, Salamov A, Chan S, Quandt CA, Foster B, Meier-Kolthoff JP, Tang YT, Schwientek P, Benny GL, Smith ME, Bauer D, Deshpande S, et al. A single-cell genomics pipeline for environmental microbial eukaryotes. Iscience. 24: 102290. PMID 33870123 DOI: 10.1016/j.isci.2021.102290   
2021 Almubaid Z, Al-Mubaid H. Analysis and comparison of genetic variants and mutations of the novel coronavirus SARS-CoV-2. Gene Reports. 23: 101064. PMID 33681535 DOI: 10.1016/j.genrep.2021.101064   
2021 O'Loughlin SM, Forster AJ, Fuchs S, Dottorini T, Nolan T, Crisanti A, Burt A. Ultra-conserved sequences in the genomes of highly diverse Anopheles mosquitoes, with implications for malaria vector control. G3 (Bethesda, Md.). PMID 33730159 DOI: 10.1093/g3journal/jkab086   
2021 Martin AR, Atkinson EG, Chapman SB, Stevenson A, Stroud RE, Abebe T, Akena D, Alemayehu M, Ashaba FK, Atwoli L, Bowers T, Chibnik LB, Daly MJ, DeSmet T, Dodge S, ... , et al. Low-coverage sequencing cost-effectively detects known and novel variation in underrepresented populations. American Journal of Human Genetics. PMID 33770507 DOI: 10.1016/j.ajhg.2021.03.012   
2021 Mascher M, Wicker T, Jenkins J, Plott C, Lux T, Koh CS, Ens J, Gundlach H, Boston LB, Tulpová Z, Holden S, Hernández-Pinzón I, Scholz U, Mayer KFX, Spannagl M, et al. Long-read sequence assembly: a technical evaluation in barley. The Plant Cell. PMID 33710295 DOI: 10.1093/plcell/koab077   
2021 Zhu T, Wang L, Rimbert H, Rodriguez JC, Deal KR, De Oliveira R, Choulet F, Keeble-Gagnère G, Tibbits J, Rogers J, Eversole K, Appels R, Gu YQ, Mascher M, Dvorak J, et al. Optical maps refine the bread wheat Triticum aestivum cv Chinese Spring genome assembly. The Plant Journal : For Cell and Molecular Biology. PMID 33893684 DOI: 10.1111/tpj.15289   
2021 Fu W, Wang R, Yu J, Hu D, Cai Y, Shao J, Jiang Y. GGVD: A goat genome variation database for tracking the dynamic evolutionary process of selective signatures and ancient introgressions. Journal of Genetics and Genomics = Yi Chuan Xue Bao. PMID 33965348 DOI: 10.1016/j.jgg.2021.03.003   
2021 He X, Zheng Z, Wang Q, Zhou M, Liao G, Ge Y, Cheng R. Complete chloroplast genome sequence of the medicinal plant ramie ( L. gaud) and its phylogenetic relationship to other Urticaceae species. Mitochondrial Dna. Part B, Resources. 6: 1136-1137. PMID 33796767 DOI: 10.1080/23802359.2021.1878959   
2021 Therrien DA, Konganti K, Gill JJ, Davis BW, Hillhouse AE, Michalik J, Cross HR, Smith GC, Taylor TM, Riggs PK. Complete Whole Genome Sequences of Surrogate Strains and Comparison of Sequence Methods with Application to the Food Industry. Microorganisms. 9. PMID 33809423 DOI: 10.3390/microorganisms9030608   
2021 Wang H, Wang Y, Cheng H, Xue M, Wang J, Yue Z. The complete chloroplast genome of (Benth.) Briq., a traditional Chinese herb. Mitochondrial Dna. Part B, Resources. 6: 907-908. PMID 33796676 DOI: 10.1080/23802359.2021.1886884   
2021 Zhang D, Rheindt FE, She H, Cheng Y, Song G, Jia C, Qu Y, Alström P, Lei F. Most genomic loci misrepresent the phylogeny of an avian radiation because of ancient gene flow. Systematic Biology. PMID 33787929 DOI: 10.1093/sysbio/syab024   
2021 Qian S, Zhang Y, Lee SY. Comparative Analysis of Complete Chloroplast Genome Sequences in (Thymelaeaceae) and New Insights Into Phylogenetic Relationships. Frontiers in Genetics. 12: 643552. PMID 33790948 DOI: 10.3389/fgene.2021.643552   
2021 Qian S, Zhang Y, Lee SY. Comparative Analysis of Complete Chloroplast Genome Sequences in (Thymelaeaceae) and New Insights Into Phylogenetic Relationships. Frontiers in Genetics. 12: 643552. PMID 33790948 DOI: 10.3389/fgene.2021.643552   
2021 Bhattacharyya T, Sowdhamini R. Genome-wide survey of tyrosine phosphatases in thirty mammalian genomes. Cellular Signalling. 110009. PMID 33848580 DOI: 10.1016/j.cellsig.2021.110009   
2021 Rao G, Zhang J, Liu X, Lin C, Xin H, Xue L, Wang C. De novo assembly of a new Olea europaea genome accession using nanopore sequencing. Horticulture Research. 8: 64. PMID 33790235 DOI: 10.1038/s41438-021-00498-y   
2021 Rao G, Zhang J, Liu X, Lin C, Xin H, Xue L, Wang C. De novo assembly of a new Olea europaea genome accession using nanopore sequencing. Horticulture Research. 8: 64. PMID 33790235 DOI: 10.1038/s41438-021-00498-y   
2021 Lamichhaney S, Catullo R, Keogh JS, Clulow S, Edwards SV, Ezaz T. A bird-like genome from a frog: Mechanisms of genome size reduction in the ornate burrowing frog, . Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33836564 DOI: 10.1073/pnas.2011649118   
2021 Bernard G, Stephens TG, González-Pech RA, Chan CX. Inferring Phylogenomic Relationship of Microbes Using Scalable Alignment-Free Methods. Methods in Molecular Biology (Clifton, N.J.). 2242: 69-76. PMID 33961218 DOI: 10.1007/978-1-0716-1099-2_5   
2021 Yang F, Zhang J, Wang S, Sun Z, Zhou J, Li F, Liu Y, Ding L, Liu Y, Chi W, Liu T, He Y, Xiang P, Bao Z, Olszewski MA, et al. Genomic population structure of Shanghai isolates and identification of genomic features uniquely linked with pathogenicity. Virulence. 12: 1258-1270. PMID 33904371 DOI: 10.1080/21505594.2021.1920762   
2021 Cheng J, Siejka-Zielińska P, Liu Y, Chandran A, Kriaucionis S, Song CX. Endonuclease enrichment TAPS for cost-effective genome-wide base-resolution DNA methylation detection. Nucleic Acids Research. PMID 33905495 DOI: 10.1093/nar/gkab291   
2021 Kayani MUR, Huang W, Feng R, Chen L. Genome-resolved metagenomics using environmental and clinical samples. Briefings in Bioinformatics. PMID 33758906 DOI: 10.1093/bib/bbab030   
2021 Rehder C, Bean LJH, Bick D, Chao E, Chung W, Das S, O'Daniel J, Rehm H, Shashi V, Vincent LM, . Next-generation sequencing for constitutional variants in the clinical laboratory, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 33927380 DOI: 10.1038/s41436-021-01139-4   
2021 Corpas M, Megy K, Mistry V, Metastasio A, Lehmann E. Whole Genome Interpretation for a Family of Five. Frontiers in Genetics. 12: 535123. PMID 33763108 DOI: 10.3389/fgene.2021.535123   
2021 Zhou F, Lan K, Li X, Mei Y, Cai S, Wang J. The complete chloroplast genome sequence of Delile. Mitochondrial Dna. Part B, Resources. 6: 1134-1135. PMID 33796766 DOI: 10.1080/23802359.2021.1902411