Scholarly & Creative Works
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 MortalityFull Text via DOI: 10.1111/jeu.70065 Web of Science: 001728980000010
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2025Pseudovibrio ascidiaceicola 5337, a marine bacterial symbiont of the ascidian gut with unusual genome featuresFull 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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2024Limited potexvirus diversity in eastern Gulf of Mexico seagrass meadowsFull 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 metagenomesFull 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 studiesFull Text via DOI: 10.1002/edn3.187
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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 womenFull Text via DOI: 10.1002/mbo3.1134 Web of Science: 000590331400001
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2019Taxonomic and functional heterogeneity of the gill microbiome in a symbiotic coastal mangrove lucinid species. 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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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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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 B-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. 579-591.Full Text via DOI: 10.1093/bib/bbp023 Web of Science: 000269017300010
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Contact
full name
- Shen Jean Lim
Identifiers
ORCID iD
- https://orcid.org/0000-0003-4578-5318 (confirmed)
