Andrew D. Kern - Related publications

Institute of Ecology and Evolution University of Oregon, Eugene, OR, United States 
Population and Comparative Genomics
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50 most relevant papers in past 60 days:
Year Citation  Score
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 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 Power JJ, Pinheiro F, Pompei S, Kovacova V, Yüksel M, Rathmann I, Förster M, Lässig M, Maier B. Adaptive evolution of hybrid bacteria by horizontal gene transfer. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33649202 DOI: 10.1073/pnas.2007873118   
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 Chase MA, Ellegren H, Mugal CF. Positive selection plays a major role in shaping signatures of differentiation across the genomic landscape of two independent Ficedula flycatcher species pairs. Evolution; International Journal of Organic Evolution. PMID 33851440 DOI: 10.1111/evo.14234   
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 Yang C, Zhou Y, Marcus S, Formenti G, Bergeron LA, Song Z, Bi X, Bergman J, Rousselle MMC, Zhou C, Zhou L, Deng Y, Fang M, Xie D, Zhu Y, et al. Evolutionary and biomedical insights from a marmoset diploid genome assembly. Nature. PMID 33910227 DOI: 10.1038/s41586-021-03535-x   
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 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 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 Fanelli V, Ngo KJ, Thompson VL, Silva BR, Tsai H, Sabetta W, Montemurro C, Comai L, Harmer SL. A TILLING by sequencing approach to identify induced mutations in sunflower genes. Scientific Reports. 11: 9885. PMID 33972605 DOI: 10.1038/s41598-021-89237-w   
2021 Park HJ, Gokhale CS, Bertels F. How sequence populations persist inside bacterial genomes. Genetics. PMID 33724360 DOI: 10.1093/genetics/iyab027   
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 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 Horesh G, Blackwell GA, Tonkin-Hill G, Corander J, Heinz E, Thomson NR. A comprehensive and high-quality collection of genomes and their genes. Microbial Genomics. 7. PMID 33417534 DOI: 10.1099/mgen.0.000499   
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 Cattel J, Haberkorn C, Laporte F, Gaude T, Cumer T, Renaud J, Sutherland IW, Hertz JC, Bonneville JM, Arnaud V, Fustec B, Boyer S, Marcombe S, David JP. A genomic amplification affecting a carboxylesterase gene cluster confers organophosphate resistance in the mosquito : From genomic characterization to high-throughput field detection. Evolutionary Applications. 14: 1009-1022. PMID 33897817 DOI: 10.1111/eva.13177   
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 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 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 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 Silberstein M, Nesbit N, Cai J, Lee PH. Pathway analysis for genome-wide genetic variation data: Analytic principles, latest developments, and new opportunities. Journal of Genetics and Genomics = Yi Chuan Xue Bao. PMID 33896739 DOI: 10.1016/j.jgg.2021.01.007   
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 Wang M, Zhang L, Wang Z. Chromosomal-level reference genome of the neotropical tree Jacaranda mimosifolia D. Don. Genome Biology and Evolution. PMID 33944940 DOI: 10.1093/gbe/evab094   
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 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 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 Arora D, Srikanth K, Lee J, Lee D, Park N, Wy S, Kim H, Park JE, Chai HH, Lim D, Cho IC, Kim J, Park W. Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon. Scientific Reports. 11: 7219. PMID 33785872 DOI: 10.1038/s41598-021-86683-4   
2021 Roy NS, Ramekar RV, Kim NS. Sequence-Specific Amplified Polymorphism (SSAP) and Sequence Characterized Amplified Region (SCAR) Markers in Zea mays. Methods in Molecular Biology (Clifton, N.J.). 2250: 207-218. PMID 33900607 DOI: 10.1007/978-1-0716-1134-0_20   
2021 Han Z, Liu M, Liu Q, Zhai H, Xiao S, Gao T. Chromosome-level genome assembly of burbot (Lota lota) provides insights into the evolutionary adaptations in freshwater. Molecular Ecology Resources. PMID 33730415 DOI: 10.1111/1755-0998.13382   
2021 Jiang M, Wang J, Chen M, Zhang H. Complete chloroplast genome of a rare and endangered plant species : genomic features and phylogenetic relationships with other Rosaceae plants. Mitochondrial Dna. Part B, Resources. 6: 762-768. PMID 33763572 DOI: 10.1080/23802359.2021.1881835   
2021 Lim SY, Jang JH, Lee HJ, Park SS, Kim SR, Lee KM, Kim JK, Park H, Jung HK. Characteristics and phylogenetic analysis of the complete chloroplast genome of (Paeoniaceae). Mitochondrial Dna. Part B, Resources. 6: 734-735. PMID 33763563 DOI: 10.1080/23802359.2020.1860718   
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 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 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 Walker CR, Scally A, De Maio N, Goldman N. Short-range template switching in great ape genomes explored using pair hidden Markov models. Plos Genetics. 17: e1009221. PMID 33651813 DOI: 10.1371/journal.pgen.1009221   
2021 Lu JJ, He EQ, Bao WQ, Chen JS, Sun SR, Gao SJ. Comparative genomics reveals insights into genetic variability and molecular evolution among sugarcane yellow leaf virus populations. Scientific Reports. 11: 7149. PMID 33785787 DOI: 10.1038/s41598-021-86472-z   
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 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 Zhang D, Lam J, Blobel GA. Engineering three-dimensional genome folding. Nature Genetics. PMID 33958782 DOI: 10.1038/s41588-021-00860-9   
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 Jiang M, Li Y, Chen H, Wang B, Liu C. Comparative and phylogenetic analysis of the complete chloroplast genome sequences of and . Mitochondrial Dna. Part B, Resources. 6: 1498-1506. PMID 33969207 DOI: 10.1080/23802359.2021.1911700   
2021 Generalovic TN, McCarthy SA, Warren IA, Wood JMD, Torrance J, Sims Y, Quail M, Howe K, Pipan M, Durbin R, Jiggins CD. A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.). G3 (Bethesda, Md.). PMID 33734373 DOI: 10.1093/g3journal/jkab085   
2021 Atak ZK, Taskiran II, Demeulemeester J, Flerin C, Mauduit D, Minnoye L, Hulselmans G, Christiaens V, Ghanem GE, Wouters J, Aerts S. Interpretation of allele-specific chromatin accessibility using cell state-aware deep learning. Genome Research. PMID 33832990 DOI: 10.1101/gr.260851.120   
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 van Kruistum H, Nijland R, Reznick DN, Groenen MAM, Megens HJ, Pollux BJA. Parallel genomic changes drive repeated evolution of placentas in live-bearing fish. Molecular Biology and Evolution. PMID 33620468 DOI: 10.1093/molbev/msab057   
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 Serres-Armero A, Davis BW, Povolotskaya IS, Morcillo-Suarez C, Plassais J, Juan D, Ostrander EA, Marques-Bonet T. Copy number variation underlies complex phenotypes in domestic dog breeds and other canids. Genome Research. PMID 33863806 DOI: 10.1101/gr.266049.120   
2021 Christmas MJ, Jones JC, Olsson A, Wallerman O, Bunikis I, Kierczak M, Peona V, Whitley KM, Larva T, Suh A, Miller-Struttmann NE, Geib JC, Webster MT. Genetic barriers to historical gene flow between cryptic species of alpine bumblebees revealed by comparative population genomics. Molecular Biology and Evolution. PMID 33823537 DOI: 10.1093/molbev/msab086