Publications
selected scholarly works & creative activities
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Article
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2026Genetic Features of the Scuticociliate Pathogen Philaster sp. Isolate FWC2 That Causes Sea Urchin Mass Mortality. Journal of Eukaryotic Microbiology. 73.Full Text via DOI: 10.1111/jeu.70065 Web of Science: 001728980000010
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2026The chromosomal genome sequence of the buttercup lucine, Anodontia alba Link, 1807 (Lucinida: Lucinidae) and its associated microbial metagenome sequences. Wellcome Open Research. 11.Full Text via DOI: 10.12688/wellcomeopenres.25920.1
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2025Draft genome sequence of Gracilimonas sp. strain BCB1 isolated from the gill tissue of the lucinid bivalve Stewartia floridana in Pinellas County, Florida, USA. Microbiology Resource Announcements. 14.Full Text via DOI: 10.1128/mra.00595-25 Web of Science: 001579331800001
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2025Pseudovibrio ascidiaceicola 5337, a marine bacterial symbiont of the ascidian gut with unusual genome features. Microbiology Resource Announcements. 14.Full Text via DOI: 10.1128/mra.00594-25 Web of Science: 001541888100001
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2025Prophage regulation of <i>Shewanella fidelis</i> 3313 motility and biofilm formation with implications for gut colonization dynamics in <i>Ciona robusta</i>.. eLife. 14:RP103107.Full Text via DOI: 10.7554/elife.103107
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2025Variation in accessory and horizontal gene transfer-associated genes drives lucinid endosymbiont diversity. FEMS Microbiology Ecology. 101.Full Text via DOI: 10.1093/femsec/fiaf074
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2025Diverse ssRNA viruses associated with Karenia brevis harmful algal blooms in southwest Florida. mSphere. 10.Full Text via DOI: 10.1128/msphere.01090-24 Web of Science: 001448119900001
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2024Consensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communities. Frontiers in Virology. 4.Full Text via DOI: 10.3389/fviro.2024.1371958
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2024Limited potexvirus diversity in eastern Gulf of Mexico seagrass meadows. Journal of General Virology. 105.Full Text via DOI: 10.1099/jgv.0.002004 Web of Science: 001254325600004
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2023Investigation of machine learning algorithms for taxonomic classification of marine metagenomes. Microbiology spectrum. 11.Full Text via DOI: 10.1128/spectrum.05237-22 Web of Science: 001107303900244
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2023Associations of Microbial Diversity with Age and Other Clinical Variables among Pediatric Chronic Rhinosinusitis (CRS) Patients. Microorganisms. 11.Full Text via DOI: 10.3390/microorganisms11020422
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2023Genetic features of the marine polychaete Sirsoe methanicola from metagenomic data. Frontiers in Marine Science. 9.Full Text via DOI: 10.3389/fmars.2022.1067482 Web of Science: 000919243400001
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2022Dominance of Sulfurospirillum in Metagenomes Associated with the Methane Ice Worm (Sirsoe methanicola). Applied and Environmental Microbiology. 88.Full Text via DOI: 10.1128/aem.00290-22 Web of Science: 000825366000006
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2022Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake. GigaScience. 11.Full Text via DOI: 10.1093/gigascience/giac066 Web of Science: 000846739000080
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2021Mitohelper: A mitochondrial reference sequence analysis tool for fish eDNA studies. Environmental DNA. 3:706-715.Full Text via DOI: 10.1002/edn3.187
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2021Metagenomes, metatranscriptomes, and metagenome-assembled genomes from chesapeake and Delaware bay (USA) water samples. Microbiology Resource Announcements. 10.Full Text via DOI: 10.1128/MRA.00262-21
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2021Gill microbiome structure and function in the chemosymbiotic coastal lucinid Stewartia floridana. FEMS Microbiology Ecology. 97.Full Text via DOI: 10.1093/femsec/fiab042 Web of Science: 000644508800019
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2021The Effects of Genetic Relatedness on the Preterm Infant Gut Microbiota. Microorganisms. 9.Full Text via DOI: 10.3390/microorganisms9020278 Web of Science: 000622838900001
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2020Gene expression responses to Zika virus infection in peripheral blood mononuclear cells from pregnant and non-pregnant women. MicrobiologyOpen. 9.Full Text via DOI: 10.1002/mbo3.1134 Web of Science: 000590331400001
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2020Gut microbiota differences in Island Hispanic Puerto Ricans and mainland non-Hispanic whites during chemoradiation for rectal cancer: A pilot study. Current Problems in Cancer. 44.Full Text via DOI: 10.1016/j.currproblcancer.2020.100551 Web of Science: 000553458500011
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2019Taxonomic and functional heterogeneity of the gill microbiome in a symbiotic coastal mangrove lucinid species. The ISME Journal. 13:902-920.Full Text via DOI: 10.1038/s41396-018-0318-3 Web of Science: 000461719600005
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2013Simple re-instantiation of small databases using cloud computing. BMC Genomics. 14.Full Text via DOI: 10.1186/1471-2164-14-S5-S13 Web of Science: 000329440600012
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2012Immunoinformatics: How in silico methods are re-shaping the investigation of peptide immune specificity. Frontiers in Bioscience - Elite. 4 E:311-319.Full Text via DOI: 10.2741/378
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2009A proposed minimum skill set for university graduates to meet the informatics needs and challenges of the "-omics" era. BMC Genomics. 10.Full Text via DOI: 10.1186/1471-2164-10-S3-S36
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2009Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information. Bioinformatics. 25:979-980.Full Text via DOI: 10.1093/bioinformatics/btp077 Web of Science: 000264651800028
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2009The implementation of e-learning tools to enhance undergraduate bioinformatics teaching and learning: a case study in the National University of Singapore. BMC Bioinformatics. 10.Full Text via DOI: 10.1186/1471-2105-10-S15-S12 Web of Science: 000272333800012
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Book Chapter
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2025Genome Annotation: Perspective From Bacterial Genomes. Vol6-V252.Full Text via DOI: 10.1016/B978-0-323-95502-7.00256-6
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2025Mapping the Environmental Microbiome. Vol6-V543.Full Text via DOI: 10.1016/B978-0-323-95502-7.00242-6
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Conference
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2008The value of position-specific scoring matrices for assessment of protein allegenicity. BMC Bioinformatics.Full Text via DOI: 10.1186/1471-2105-9-S12-S21 Web of Science: 000262154300021
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Other Scholarly Work
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2020Correction: Taxonomic and functional heterogeneity of the gill microbiome in a symbiotic coastal mangrove lucinid species (The ISME Journal, (2019), 13, 4, (902-920), 10.1038/s41396-018-0318-3). The ISME Journal. 1063-1064.Full Text via DOI: 10.1038/s41396-020-0585-7
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Preprint
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2023Limited potexvirus diversity in eastern Gulf of Mexico seagrass meadowsFull Text via DOI: 10.1101/2023.12.11.571111
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Review
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2020An introduction to phylosymbiosis. Proceedings of the Royal Society of London. Biological Sciences.Full Text via DOI: 10.1098/rspb.2019.2900 Web of Science: 000521569300007
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2009Recent advances in computer-aided drug design. Briefings in Bioinformatics. 579-591.Full Text via DOI: 10.1093/bib/bbp023 Web of Science: 000269017300010
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Contact
full name
- Shen Jean Lim
