| Year |
Citation |
Score |
| 2023 |
Sahu N, Indic B, Wong-Bajracharya J, Merényi Z, Ke HM, Ahrendt S, Monk TL, Kocsubé S, Drula E, Lipzen A, Bálint B, Henrissat B, Andreopoulos B, Martin FM, Bugge Harder C, ... ... Tsai IJ, et al. Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria. Nature Microbiology. PMID 37550506 DOI: 10.1038/s41564-023-01448-1 |
0.342 |
|
| 2023 |
Lee YC, Ke HM, Liu YC, Lee HH, Wang MC, Tseng YC, Kikuchi T, Tsai IJ. Single-worm long-read sequencing reveals genome diversity in free-living nematodes. Nucleic Acids Research. PMID 37526286 DOI: 10.1093/nar/gkad647 |
0.529 |
|
| 2023 |
Lai CK, Lee YC, Ke HM, Lu MR, Liu WA, Lee HH, Liu YC, Yoshiga T, Kikuchi T, Chen PJ, Tsai IJ. The Aphelenchoides genomes reveal substantial horizontal gene transfers in the last common ancestor of free-living and major plant parasitic nematodes. Molecular Ecology Resources. PMID 36597348 DOI: 10.1111/1755-0998.13752 |
0.465 |
|
| 2022 |
Hoh DZ, Lee HH, Wada N, Liu WA, Lu MR, Lai CK, Ke HM, Sun PF, Tang SL, Chung WH, Chen YL, Chung CL, Tsai IJ. Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization. Bmc Biology. 20: 236. PMID 36266645 DOI: 10.1186/s12915-022-01436-7 |
0.785 |
|
| 2022 |
Tsai IJ. The teenage years of yeast population genomics trace history, admixing and getting wilder. Current Opinion in Genetics & Development. 75: 101942. PMID 35753210 DOI: 10.1016/j.gde.2022.101942 |
0.427 |
|
| 2022 |
De Vivo M, Lee HH, Huang YS, Dreyer N, Fong CL, de Mattos FMG, Jain D, Wen YV, Mwihaki JK, Wang TY, Machida RJ, Wang J, Chan BKK, Tsai IJ. Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum. Scientific Reports. 12: 9973. PMID 35705661 DOI: 10.1038/s41598-022-14121-0 |
0.411 |
|
| 2022 |
Ng CS, Lai CK, Ke HM, Lee HH, Chen CF, Tang PC, Cheng HC, Lu MJ, Li WH, Tsai IJ. Genome Assembly and Evolutionary Analysis of the Mandarin Duck Aix galericulata Reveal Strong Genome Conservation among Ducks. Genome Biology and Evolution. 14. PMID 35640266 DOI: 10.1093/gbe/evac083 |
0.741 |
|
| 2022 |
Lee TJ, Liu Y, Liu WA, Lin YF, Lee HH, Ke HM, Huang JP, Lu MJ, Hsieh CL, Chung KF, Liti G, Tsai IJ. Extensive sampling of in Taiwan reveals ecology and evolution of predomesticated lineages. Genome Research. PMID 35361625 DOI: 10.1101/gr.276286.121 |
0.312 |
|
| 2022 |
Mozzachiodi S, Bai FY, Baldrian P, Bell G, Boundy-Mills K, Buzzini P, Čadež N, Cubillos FA, Dashko S, Dimitrov R, Fisher KJ, Gibson B, Gouliamova D, Greig D, Heistinger L, ... ... Tsai IJ, et al. Yeasts from temperate forests. Yeast (Chichester, England). PMID 35146791 DOI: 10.1002/yea.3699 |
0.444 |
|
| 2020 |
Cheng YH, Liu CJ, Yu YH, Jhou YT, Fujishima M, Tsai IJ, Leu JY. Genome plasticity in Paramecium bursaria revealed by population genomics. Bmc Biology. 18: 180. PMID 33250052 DOI: 10.1186/s12915-020-00912-2 |
0.503 |
|
| 2020 |
Ke HM, Lee HH, Lin CI, Liu YC, Lu MR, Hsieh JA, Chang CC, Wu PH, Lu MJ, Li JY, Shang G, Lu RJ, Nagy LG, Chen PY, Kao HW, ... Tsai IJ, et al. genomes resolve the evolution of fungal bioluminescence. Proceedings of the National Academy of Sciences of the United States of America. PMID 33229585 DOI: 10.1073/pnas.2010761117 |
0.447 |
|
| 2020 |
Dayi M, Sun S, Maeda Y, Tanaka R, Yoshida A, Tsai IJ, Kikuchi T. Nearly Complete Genome Assembly of the Pinewood Nematode Bursaphelenchus xylophilus Strain Ka4C1. Microbiology Resource Announcements. 9. PMID 33060277 DOI: 10.1128/MRA.01002-20 |
0.407 |
|
| 2019 |
Lee HH, Ke HM, Lin CI, Lee TJ, Chung CL, Tsai IJ. Evidence of extensive intraspecific noncoding reshuffling in a 169-kb mitochondrial genome of a basidiomycetous fungus. Genome Biology and Evolution. PMID 31418013 DOI: 10.1093/gbe/evz181 |
0.435 |
|
| 2019 |
Chaw SM, Liu YC, Wu YW, Wang HY, Lin CI, Wu CS, Ke HM, Chang LY, Hsu CY, Yang HT, Sudianto E, Hsu MH, Wu KP, Wang LN, Leebens-Mack JH, ... Tsai IJ, et al. Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution. Nature Plants. 5: 63-73. PMID 30626928 DOI: 10.1038/s41477-018-0337-0 |
0.524 |
|
| 2018 |
Kanzaki N, Tsai IJ, Tanaka R, Hunt VL, Liu D, Tsuyama K, Maeda Y, Namai S, Kumagai R, Tracey A, Holroyd N, Doyle SR, Woodruff GC, Murase K, Kitazume H, et al. Biology and genome of a newly discovered sibling species of Caenorhabditis elegans. Nature Communications. 9: 3216. PMID 30097582 DOI: 10.1038/S41467-018-05712-5 |
0.751 |
|
| 2018 |
Ke HM, Liu D, Ogura Y, Hayashi T, Urbanczyk H, Tsai IJ. Tracing genomic divergence ofbacteria in the Harveyi clade. Journal of Bacteriology. PMID 29555692 DOI: 10.1128/JB.00001-18 |
0.461 |
|
| 2018 |
Liu D, Hunt M, Tsai IJ. Inferring synteny between genome assemblies: a systematic evaluation. Bmc Bioinformatics. 19: 26. PMID 29382321 DOI: 10.1186/s12859-018-2026-4 |
0.771 |
|
| 2017 |
Chung CL, Lee TJ, Akiba M, Lee HH, Kuo TH, Liu D, Ke HM, Yokoi T, Roa MB, Lu MJ, Chang YY, Ann PJ, Tsai JN, Chen CY, Tzean SS, ... ... Tsai IJ, et al. Comparative and population genomics landscape of Phellinus noxius: a hypervariable fungus causing root rot in trees. Molecular Ecology. PMID 28926153 DOI: 10.1111/mec.14359 |
0.437 |
|
| 2017 |
Ke HM, Prachumwat A, Yu CP, Yang YT, Promsri S, Liu KF, Lo CF, Lu MJ, Lai MC, Tsai IJ, Li WH. Comparative genomics of Vibrio campbellii strains and core species of the Vibrio Harveyi clade. Scientific Reports. 7: 41394. PMID 28145490 DOI: 10.1038/srep41394 |
0.765 |
|
| 2016 |
Cotton JA, Steinbiss S, Yokoi T, Tsai IJ, Kikuchi T. An expressed, endogenous Nodavirus-like element captured by a retrotransposon in the genome of the plant parasitic nematode Bursaphelenchus xylophilus. Scientific Reports. 6: 39749. PMID 28004836 DOI: 10.1038/Srep39749 |
0.41 |
|
| 2016 |
Cotton JA, Bennuru S, Grote A, Harsha B, Tracey A, Beech R, Doyle SR, Dunn M, Hotopp JC, Holroyd N, Kikuchi T, Lambert O, Mhashilkar A, Mutowo P, Nursimulu N, ... ... Tsai IJ, et al. The genome of Onchocerca volvulus, agent of river blindness. Nature Microbiology. 2: 16216. PMID 27869790 DOI: 10.1038/Nmicrobiol.2016.216 |
0.74 |
|
| 2016 |
Suttiprapa S, Rinaldi G, Tsai IJ, Mann VH, Dubrovsky L, Yan HB, Holroyd N, Huckvale T, Durrant C, Protasio AV, Pushkarsky T, Iordanskiy S, Berriman M, Bukrinsky MI, Brindley PJ. HIV-1 Integrates Widely throughout the Genome of the Human Blood Fluke Schistosoma mansoni. Plos Pathogens. 12: e1005931. PMID 27764257 DOI: 10.1371/Journal.Ppat.1005931 |
0.76 |
|
| 2016 |
Hunt VL, Tsai IJ, Selkirk ME, Viney M. The genome of Strongyloides spp. gives insights into protein families with a putative role in nematode parasitism. Parasitology. 1-16. PMID 27618747 DOI: 10.1017/S0031182016001554 |
0.374 |
|
| 2016 |
Wu GL, Kuo TH, Tsay TT, Tsai IJ, Chen PJ. Glycoside Hydrolase (GH) 45 and 5 Candidate Cellulases in Aphelenchoides besseyi Isolated from Bird's-Nest Fern. Plos One. 11: e0158663. PMID 27391812 DOI: 10.1371/journal.pone.0158663 |
0.306 |
|
| 2016 |
Hunt VL, Tsai IJ, Coghlan A, Reid AJ, Holroyd N, Foth BJ, Tracey A, Cotton JA, Stanley EJ, Beasley H, Bennett HM, Brooks K, Harsha B, Kajitani R, Kulkarni A, et al. The genomic basis of parasitism in the Strongyloides clade of nematodes. Nature Genetics. PMID 26829753 DOI: 10.1038/Ng.3495 |
0.763 |
|
| 2015 |
Palomares-Rius JE, Tsai IJ, Karim N, Akiba M, Kato T, Maruyama H, Takeuchi Y, Kikuchi T. Genome-wide variation in the pinewood nematode Bursaphelenchus xylophilus and its relationship with pathogenic traits. Bmc Genomics. 16: 845. PMID 26493074 DOI: 10.1186/s12864-015-2085-0 |
0.467 |
|
| 2015 |
Koufopanou V, Lomas S, Tsai IJ, Burt A. Estimating the fitness effects of new mutations in the wild yeast Saccharomyces paradoxus. Genome Biology and Evolution. PMID 26085542 DOI: 10.1093/Gbe/Evv112 |
0.463 |
|
| 2014 |
Bennett HM, Mok HP, Gkrania-Klotsas E, Tsai IJ, Stanley EJ, Antoun NM, Coghlan A, Harsha B, Traini A, Ribeiro DM, Steinbiss S, Lucas SB, Allinson KS, Price SJ, Santarius TS, et al. The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion. Genome Biology. 15: 510. PMID 25413302 DOI: 10.1186/S13059-014-0510-3 |
0.689 |
|
| 2014 |
Foth BJ, Tsai IJ, Reid AJ, Bancroft AJ, Nichol S, Tracey A, Holroyd N, Cotton JA, Stanley EJ, Zarowiecki M, Liu JZ, Huckvale T, Cooper PJ, Grencis RK, Berriman M. Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction. Nature Genetics. 46: 693-700. PMID 24929830 DOI: 10.1038/Ng.3010 |
0.808 |
|
| 2014 |
Palomares-Rius JE, Hirooka Y, Tsai IJ, Masuya H, Hino A, Kanzaki N, Jones JT, Kikuchi T. Distribution and evolution of glycoside hydrolase family 45 cellulases in nematodes and fungi Bmc Evolutionary Biology. 14. PMID 24690293 DOI: 10.1186/1471-2148-14-69 |
0.317 |
|
| 2014 |
Tsai IJ, Tanaka E, Masuya H, Tanaka R, Hirooka Y, Endoh R, Sahashi N, Kikuchi T. Comparative genomics of taphrina fungi causing varying degrees of tumorous deformity in plants Genome Biology and Evolution. 6: 861-872. PMID 24682155 DOI: 10.1093/gbe/evu067 |
0.311 |
|
| 2014 |
Cotton JA, Lilley CJ, Jones LM, Kikuchi T, Reid AJ, Thorpe P, Tsai IJ, Beasley H, Blok V, Cock PJ, Eves-van den Akker S, Holroyd N, Hunt M, Mantelin S, Naghra H, et al. The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biology. 15: R43. PMID 24580726 DOI: 10.1186/Gb-2014-15-3-R43 |
0.801 |
|
| 2014 |
Tsai IJ, Hunt M, Holroyd N, Huckvale T, Berriman M, Kikuchi T. Summarizing specific profiles in illumina sequencing from whole-genome amplified DNA Dna Research. 21: 243-254. PMID 24353264 DOI: 10.1093/Dnares/Dst054 |
0.746 |
|
| 2013 |
Valentim CL, Cioli D, Chevalier FD, Cao X, Taylor AB, Holloway SP, Pica-Mattoccia L, Guidi A, Basso A, Tsai IJ, Berriman M, Carvalho-Queiroz C, Almeida M, Aguilar H, Frantz DE, et al. Genetic and molecular basis of drug resistance and species-specific drug action in schistosome parasites. Science (New York, N.Y.). 342: 1385-9. PMID 24263136 DOI: 10.1126/Science.1243106 |
0.534 |
|
| 2013 |
Laing R, Kikuchi T, Martinelli A, Tsai IJ, Beech RN, Redman E, Holroyd N, Bartley DJ, Beasley H, Britton C, Curran D, Devaney E, Gilabert A, Hunt M, Jackson F, et al. The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery. Genome Biology. 14: R88. PMID 23985316 DOI: 10.1186/Gb-2013-14-8-R88 |
0.807 |
|
| 2013 |
Tsai IJ, Zarowiecki M, Holroyd N, Garciarrubio A, Sanchez-Flores A, Brooks KL, Tracey A, Bobes RJ, Fragoso G, Sciutto E, Aslett M, Beasley H, Bennett HM, Cai J, Camicia F, et al. The genomes of four tapeworm species reveal adaptations to parasitism. Nature. 496: 57-63. PMID 23485966 DOI: 10.1038/Nature12031 |
0.786 |
|
| 2012 |
Rinaldi G, Eckert SE, Tsai IJ, Suttiprapa S, Kines KJ, Tort JF, Mann VH, Turner DJ, Berriman M, Brindley PJ. Germline transgenesis and insertional mutagenesis in Schistosoma mansoni mediated by murine leukemia virus. Plos Pathogens. 8: e1002820. PMID 22911241 DOI: 10.1371/Journal.Ppat.1002820 |
0.641 |
|
| 2012 |
Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M, Otto TD. A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nature Protocols. 7: 1260-84. PMID 22678431 DOI: 10.1038/Nprot.2012.068 |
0.665 |
|
| 2012 |
Protasio AV, Tsai IJ, Babbage A, Nichol S, Hunt M, Aslett MA, De Silva N, Velarde GS, Anderson TJ, Clark RC, Davidson C, Dillon GP, Holroyd NE, LoVerde PT, Lloyd C, et al. A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni. Plos Neglected Tropical Diseases. 6: e1455. PMID 22253936 DOI: 10.1371/Journal.Pntd.0001455 |
0.769 |
|
| 2011 |
Kikuchi T, Cotton JA, Dalzell JJ, Hasegawa K, Kanzaki N, McVeigh P, Takanashi T, Tsai IJ, Assefa SA, Cock PJ, Otto TD, Hunt M, Reid AJ, Sanchez-Flores A, Tsuchihara K, et al. Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. Plos Pathogens. 7: e1002219. PMID 21909270 DOI: 10.1371/Journal.Ppat.1002219 |
0.822 |
|
| 2011 |
Tsai IJ. Genome watch: Honey, i shrunk the mimiviral genome Nature Reviews Microbiology. 9: 563. PMID 21747393 DOI: 10.1038/nrmicro2623 |
0.456 |
|
| 2010 |
Tsai IJ, Otto TD, Berriman M. Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biology. 11: R41. PMID 20388197 DOI: 10.1186/Gb-2010-11-4-R41 |
0.602 |
|
| 2010 |
Tsai IJ, Burt A, Koufopanou V. Conservation of recombination hotspots in yeast. Proceedings of the National Academy of Sciences of the United States of America. 107: 7847-52. PMID 20385822 DOI: 10.1073/Pnas.0908774107 |
0.542 |
|
| 2009 |
Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O'Kelly MJ, van Oudenaarden A, et al. Population genomics of domestic and wild yeasts. Nature. 458: 337-41. PMID 19212322 DOI: 10.1038/Nature07743 |
0.651 |
|
| 2008 |
Tsai IJ, Bensasson D, Burt A, Koufopanou V. Population genomics of the wild yeast Saccharomyces paradoxus: Quantifying the life cycle. Proceedings of the National Academy of Sciences of the United States of America. 105: 4957-62. PMID 18344325 DOI: 10.1073/Pnas.0707314105 |
0.558 |
|
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