Lim, Shen Jean

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Lim, Shen Jean Graduate Faculty

Positions

Assistant Professor, Biological Sciences , College of Arts, Sciences & Education

shlim@fiu.edu

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selected scholarly works & creative activities

Article
- 2026
  
  Metagenomic analysis of water column samples collected from Green Canyon 233 prior to the Deepwater Horizon incident. APPLIED AND ENVIRONMENTAL MICROBIOLOGY. 92.
  Full Text via DOI: 10.1128/aem.00799-26 Web of Science: 001796500300001
- 2026
  
  Dietary Quality and Microbiome Profiles among Rectal Cancer Patients: A Cross-Sectional Pilot Study. Puerto Rico Health Sciences Journal. 45:3-10.
  Web of Science: 001731014100001
- 2026
  
  Genetic 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
- 2026
  
  The 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
- 2025
  
  Draft 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
- 2025
  
  Pseudovibrio 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
- 2025
  
  Prophage 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
- 2025
  
  Variation in accessory and horizontal gene transfer-associated genes drives lucinid endosymbiont diversity. FEMS MICROBIOLOGY ECOLOGY. 101.
  Full Text via DOI: 10.1093/femsec/fiaf074
- 2025
  
  Diverse 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
- 2024
  
  Consensus 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
- 2024
  
  Limited 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
- 2023
  
  Investigation 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
- 2023
  
  Insights from Bacterial 16S rRNA Gene into Bacterial Genera and Predicted Metabolic Pathways Associated with Stool Consistency in Rectal Cancer Patients: A Proof of Concept. BIOLOGICAL RESEARCH FOR NURSING. 25:491-500.
  Full Text via DOI: 10.1177/10998004231159623
- 2023
  
  Associations of Microbial Diversity with Age and Other Clinical Variables among Pediatric Chronic Rhinosinusitis (CRS) Patients. MICROORGANISMS. 11.
  Full Text via DOI: 10.3390/microorganisms11020422
- 2023
  
  Genetic 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
- 2022
  
  Dominance 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
- 2022
  
  Tourmaline: 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
- 2021
  
  Mitohelper: A mitochondrial reference sequence analysis tool for fish eDNA studies. Environmental DNA. 3:706-715.
  Full Text via DOI: 10.1002/edn3.187
- 2021
  
  Metagenomes, 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
- 2021
  
  Gill 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
- 2021
  
  The Effects of Genetic Relatedness on the Preterm Infant Gut Microbiota. MICROORGANISMS. 9.
  Full Text via DOI: 10.3390/microorganisms9020278 Web of Science: 000622838900001
- 2021
  
  Changes in Gut Microbiome Associated With Co-Occurring Symptoms Development During Chemo-Radiation for Rectal Cancer: A Proof of Concept Study. BIOLOGICAL RESEARCH FOR NURSING. 23:31-41.
  Full Text via DOI: 10.1177/1099800420942830
- 2020
  
  Gene 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
- 2020
  
  Gut 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
- 2019
  
  Taxonomic 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
- 2013
  
  Simple 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
- 2012
  
  Immunoinformatics: 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
- 2009
  
  A 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
- 2009
  
  Allergen 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
- 2009
  
  The 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
- Extensive Thioautotrophic Gill Endosymbiont Diversity within a Single Ctena orbiculata (Bivalvia: Lucinidae) Population and Implications for Defining Host-Symbiont Specificity and Species Recognition. MSYSTEMS. 4.
  Full Text via DOI: 10.1128/mSystems.00280-19 Web of Science: 000500491200003
Book Chapter
- 2025
  
  Genome Annotation: Perspective From Bacterial Genomes. Vol6-V252.
  Full Text via DOI: 10.1016/B978-0-323-95502-7.00256-6
- 2025
  
  Mapping the Environmental Microbiome. Vol6-V543.
  Full Text via DOI: 10.1016/B978-0-323-95502-7.00242-6
Conference
- 2008
  
  The 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
Other Scholarly Work
- 2025
  
  Incorporating microbiomes into the One Health Joint Plan of Action.. MBIO. e0145625.
  Full Text via DOI: 10.1128/mbio.01456-25
- 2025
  
  The genome sequences of the woven lucine, Lucinisca nassula (Conrad, 1846) and a bacterial endosymbiont
  Full Text via DOI: 10.12688/wellcomeopenres.24087.1
- 2020
  
  Correction: 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). ISME JOURNAL. 1063-1064.
  Full Text via DOI: 10.1038/s41396-020-0585-7
- 2020
  
  Uncovering host-microbiome interactions in global systems with collaborative programming: a novel approach integrating social and data sciences
  Full Text via DOI: 10.12688/f1000research.26459.1
Preprint
- 2026
  
  The chromosomal genome sequence of the buttercup lucine, Anodontia alba Link, 1807 (Lucinida: Lucinidae) and its associated microbial metagenome sequences
  Full Text via DOI: 10.12688/wellcomeopenres.25920.1
- 2025
  
  Prophage regulation of Shewanella fidelis 3313 motility and biofilm formation: implications for gut colonization dynamics in Ciona robusta
  Full Text via DOI: 10.7554/elife.103107.2
- 2025
  
  Prophage regulation of Shewanella fidelis 3313 motility and biofilm formation: implications for gut colonization dynamics in Ciona robusta
  Full Text via DOI: 10.7554/elife.103107.1
- 2023
  
  Limited potexvirus diversity in eastern Gulf of Mexico seagrass meadows
  Full Text via DOI: 10.1101/2023.12.11.571111
- 2022
  
  Associations of microbial diversity with age and other clinical variables among pediatric chronic rhinosinusitis (CRS) patients
  Full Text via DOI: 10.1101/2022.10.19.512947
- 2022
  
  Prophage regulation of Shewanella fidelis 3313 motility and biofilm formation: implications for gut colonization dynamics in Ciona robusta
  Full Text via DOI: 10.1101/2022.11.23.517592
- 2021
  
  Tourmaline: a containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake
  Full Text via DOI: 10.1101/2021.09.15.460495
- An introduction to phylosymbiosis
  Full Text via DOI: 10.7287/peerj.preprints.27879v1
- An introduction to phylosymbiosis
  Full Text via DOI: 10.7287/peerj.preprints.27879v2
Review
- 2020
  
  An introduction to phylosymbiosis. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES.
  Full Text via DOI: 10.1098/rspb.2019.2900 Web of Science: 000521569300007
- 2009
  
  Recent advances in computer-aided drug design. Briefings in Bioinformatics. 579-591.
  Full Text via DOI: 10.1093/bib/bbp023 Web of Science: 000269017300010

principal investigator on

Investigating the feasibility of harnessing chemosymbiotic lucinid bivalves and their symbionts for seagrass restoration in Florida awarded by Florida Department of Environmental Prot 2026 - 2027

full name

Shen Jean Lim

ORCID iD

https://orcid.org/0000-0003-4578-5318 (confirmed)

visualizations

Co-author Network

Co-investigator Network