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📰 Refereed Journal Articles

Mentee(s) highlighted in bold (* - corresponding author)

2026

• González-Mercado, V. J., Lim, S.J., Kumar Singh, P., Sales-Martinez, S., Fernandez-Cajavilca, M., Marrero, L. M., … D’Eramo Melkus, G. (2026). Dietary Quality and Microbiome Profiles among Rectal Cancer Patients: A Cross-Sectional Pilot Study. Puerto Rico Health Sciences Journal, 45(1), 3–10
• *Lim, S.J. & Breitbart, M. (2026) Genetic features of the scuticociliate pathogen Philaster sp. isolate FWC2 that causes sea urchin mass mortality. Journal of Eukaryotic Microbiology 73(2): e70065
• Chin, D., Campbell, B., Petersen, J., Lim, S.J. … Aquatic Symbiosis Genomics Project Leadership (2026) The chromosomal genome sequence of the buttercup lucine, Anodontia alba Link, 1807 (Lucinida: Lucinidae) and its associated microbial metagenome sequences. Wellcome Open Research, 11:131

2025

• *Lim, S.J., Natarajan O., Keller J., Dishaw, L.J., Furman, B.T., Breitbart, M. (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. Microbiol. Resour. Announc. 0:e00595-25
• Couradeau E., Martiny J.B.H, … the Microbiomes for One Health Initiative (2025) Incorporating microbiomes into the One Health Joint Plan of Action. mBio 0:e01456-25
• Young, M., Natarajan, O., Lim, S.J., Dishaw L.J. (2025) Pseudovibrio ascidiaceicola 5337, a marine bacterial symbiont of the ascidian gut with unusual genome features. Microbiol. Resour. Announc. 0:e00594-25
• Giani, N.M., Lim, S.J., Anderson, L.C., Paterson, A.T., Engel, A.S., Campbell, B.J. (2025) Variation in accessory and horizontal gene transfer-associated genes drives lucinid endosymbiont diversity, FEMS Microbiology Ecology 101(8):fiaf074
• *Lim, S.J., Rogers, A., Rosario, K., Kerr, M., Garrett, M., Koester, J., Hubbard, K.A., Breitbart, M. (2025) Diverse ssRNA viruses associated with Karenia brevis harmful algal blooms in Southwest Florida, mSphere 10:e01090-24

  This article is included in ASM’s Sustainable Development Goals (SDG) Spotlight collection

• Anderson, L.C., Campbell, B., Long-Fox, B., Petersen, J., Lim, S.J. … Aquatic Symbiosis Genomics Project Leadership (2025) The genome sequence of the woven lucine, Lucinisca nassula (Conrad, 1846), Wellcome Open Research, 10:225
• Natarajan, O., Gibboney, S.L., Young, M.N., Lim, S.J., Nguyen, F., Pluta, N., Atkinson, C.G.F., Liberti, A., Kees, E.D., Leigh, B.A., Breitbart, M., Gralnick, J.A. & Dishaw, L.J. (2025) Prophages regulation of Shewanella fidelis 3313 motility and biofilm formation: implications for gut colonization dynamics in Ciona robusta, eLife, 14:RP103107

2024

• *Lim, S.J., Rosario, K., Kernbach, M.E., Gross, A.J., Furman, Bradley T. & Breitbart, M. (2024) Limited potexvirus diversity in eastern Gulf of Mexico seagrass meadows, Journal of General Virology, 105(6): 002004.
• Charon, J., Olendraite, I., …, Lim, S.J., …, Neri, U. (2024) Consensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communities, Frontiers in Virology, 4 - 2024

2023

• Park, H., Lim, S.J., Cosme, J., O’Connell, K., Sandeep, J., Gayanilo, F., Cutter, G.R., Montes, E., Nitikitpaiboon, C., Fisher, S., Moustahfid, H, & Thompson, L.R. (2023) Investigation of machine learning algorithms for taxonomic classification of marine metagenomes, Microbiology spectrum, 11:e05237-22
• Gonzalez-Mercado, V.J., Lim, S.J. & Aouizerat, B. (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(3):491-500
• Lim, S.J., Jithpratuck, W., Wasylik, K., Sriaroon, P. & Dishaw, L.J. (2023) Associations of microbial diversity with age and other clinical variables among pediatric chronic rhinosinusitis (CRS) patients, Microorganisms, 11(2), 422
• *Lim, S.J., Thompson, L.R. & Goodwin, K.D. (2023) Genetic features of the marine polychaete Sirsoe methanicola from metagenomic data, Frontiers in Marine Science, 9:1067482
• Lim, S.J., Thompson, L.R., Young, C.M., Gaasterland & Goodwin, K.D. (2022) Dominance of Sulfurospirillum in metagenomes associated with the methane ice worm (Sirsoe methanicola), Applied and Environmental Microbiology, 88(15): e0029022 (spotlight selection)

2022

• Thompson, L.R., Anderson, S.R., DenUyl, P.A., Patin, N.V., Lim, S.J., Sanderson, G., Goodwin, K.D. (2022) Tourmaline: a containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake, GigaScience, 11: giac066

2021

• Gonzalez-Mercado, V.J., Lim, S.J., Yu, G., Penedo, F., Pedro, E., Bernabe, R., Tirado-Gómez, M. & Aouizerat, B. (2021) Co-occurrence of symptoms and gut microbiota composition before neoadjuvant chemotherapy and radiation therapy for rectal cancer: a proof of concept, Biological Research for Nursing, 23(3): 513-523
• Gonzalez-Mercado, V.J., Lim, S.J., Saligan, L., Sarkar, A., Perez, N., Rodriguez, C., Bernabe, R., Dutra, S.V.O., Pedro, E., Sepehri, F. & Aouizerat, B. (2021) Gut microbiota and depressive symptoms at the end of neoadjuvant chemotherapy and radiation therapy for rectal cancer: a cross-sectional pilot study, Depression Research and Treatment, 2021:7967552
• Ahmed, M.A., Lim, S.J. & Campbell, B.J. (2021) Metagenomes, metatranscriptomes and metagenome-assembled genomes (MAGs) from Chesapeake and Delaware Bay (USA) water samples, Microbiology Resource Announcements, 10(21): e0026221
• Lim, S.J., Davis, B.G., Gill, D.E., Swetenburg, J., Anderson, L.C., Engel, A.S. & Campbell, B.J. (2021) Gill microbiome structure and function in the chemosymbiotic coastal lucinid Stewartia floridana, FEMS Microbiology Ecology, 97(4): fiab042
• Lim, S.J., & Thompson, L.R. (2021) Mitohelper: A mitochondrial reference sequence analysis tool for fish eDNA studies, Environmental DNA, 3: 706-715

  GitHub repository: https://github.com/aomlomics/mitohelper | Datasets:

• Lim, S.J., Aguilar-Lopez, M., Wetzel, C., Dutra, S.V.O, Bray, V., Groer, M.W., Donovan, S.M. & Ho, T. (2021) The effects of genetic relatedness on the preterm infant gut microbiota, Microorganisms, 9(2):278
• Gonzalez-Mercado, V.J., Lim, S.J., Marrero, S.J., Pedro, E. & Saligan, L.N. (2021) Gut microbiota and fatigue in rectal cancer patients: a cross-sectional pilot study, Supportive Care in Cancer, 29:4615-4621

2020

• Lim, S.J., Seyfang, A., Dutra, S.V.O., Kane, B. & Groer M. (2020) Gene expression responses to Zika virus infection in peripheral blood mononuclear cells from pregnant and non-pregnant women. MicrobiologyOpen, 9(12): e1134
• Oberstaller, J., Gibbons, J., …, Lim, S.J., …, Jiang, R.H.Y. (2020) OneHealth codeathon of host-microbiome interactions - a novel approach integrating social sciences and data sciences, F1000 Research, 9(1478): 1478
• Gonzalez-Mercado, V.J., Henderson, W., Sarkar, A., Lim, S.J., Saligan, L.N, Berk, L.; Dishaw, L., McMillan, S., Groer, M., Sepehri, F. & Melkus, G. (2020) 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(1):31-41
• Gonzalez-Mercado, V.J., Lim, S.J., Berk, L., Esele, M., Rodriguez, C. & Colon-Otero, G. (2020) Gut microbiota differences in island Hispanic Puerto Ricans and mainland non-Hispanic whites during chemo-radiation for rectal cancer: a pilot study. Current Problems in Cancer, 10051

2018-2019

• Lim, S.J. & Bordenstein, S.R. (2019) An introduction to phylosymbiosis. Proceedings of the Royal Society B, 287: 20192900

• Lim, S.J., Alexander, L., Engel, A.S., Paterson, A.T., Anderson, L.C. & Campbell, B.J. (2019) Extensive thioautotrophic endosymbiont species diversity within a single Ctena orbiculata (Bivalvia:Lucinidae) population. mSystems, 4:e00280-19

• Lim, S.J., Davis, B.G., Gill, D.E., Walton, J., Nachman, E., Engel, A.S., Anderson, L.C. & Campbell, B.J. (2018) Taxonomic and functional heterogeneity of the gill microbiome in a symbiotic coastal mangrove lucinid species. ISME J, 13: 902-920

2009-2012

• Wee, L.J., Lim, S.J., Ng, L.F. & Tong, J.C. (2012) Immunoinformatics: how in silico methods are re-shaping the investigation of peptide immune specificity. Front Biosci (Elite Ed), 4:311-9
• Lim, S.J., Tan, T.W. & Tong, J.C. (2010) Computational epigenetics: the new scientific paradigm. Bioinformation, 4(7): 331 337
• Song, C.M., Lim, S.J. & Tong, J.C. (2009) Recent advances in computer-aided drug design. Briefings in Bioinformatics, 10(5): 579 91
• Tong, J.C., Lim, S.J. Muh, H.C., Chew, F.T. & Tammi, M.T. (2009) Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information. Bioinformatics, 25(7): 979 80

📚 Book Chapters

Mentee(s) highlighted in bold (* - corresponding author)

• *Lim, S.J. & Young, M.N. (2024) Genome annotation: perspective from bacterial genomes. In Encyclopedia of Bioinformatics and Computational Biology (Second Edition), 6: 240-252
• *Lim, S.J. (2024) Mapping the environmental microbiome. In Encyclopedia of Bioinformatics and Computational Biology (Second Edition), 6: 531-543
• Lim, S.J., Khan, A.M., De Silva, M., Lim, K.S., Hu, Y., Tan, C.H. & Tan, T.W. (2011) Integration of e-learning tools with the problem-based learning approach to enhance teaching and learning in undergraduate bioinformatics modules. In Technology in Higher Education: The State of the Art [E-Publication Volume], p.63-79.
• Tong, J.C. & Lim, S.J. (2010) Computational epigenetics. In Encyclopedia of Molecular Cell Biology and Molecular Medicine, 3rd ed., Meyers, Bob. Wiley.