Publications

In Preparation

• Ashey, J., McKelvie, H., Freeman, J., Shpilker, P., Cowen, L., Richmond, R., Paul, V., Seneca, F., Putnam, H., Sediment Stress Across Locations and Species, in preparation
• Murthy, M.H.S., Jasbi, P., Vizgaudis, W., Kumar, L., Olaosebikan, M., Roger, L., Yang, Y. Lewinski, N., Daniels, N., Cowen, L., and Klein-Seetharaman, J. (2022) Insulin Signaling and Pharmacology in Humans and in Corals, Drug Discovery Today, in preparation
• Roger, L. M., Roxbury, D., Tresguerres, M., Putnam, H., Lewinski, N., Wangpraseurt, D. Leveraging nanotechnologies to engineering coral futures – Perspective Piece. In preparation.

Under review

• Li, S., Roger, L. M., Kumar, L., Lewinski, N., Klein-Seetharaman, J., Putnam, H. M., Yang, J. (2021). Coral bleaching and tissue loss dynamics captured through the high frequency imagery. Under review in PloS ONE
• Reich, H., Roger, L. M., Camp, E. F., Putnam, H. M. Trace metals are critical to the nutritional economy of the coral holobiont. Under review in Biological Reviews
• Roger, L. M., Darko, Y. A., Bernas, T., White, F., Olaosebikan, M., Cowen, L., Klein-Seetharaman, J., Lewinski, N. Evaluation of fluorescence-based viability stains in cells dissociated from scleractinian coral Pocillopora damicornis. Under review in Scientific Reports
• Roger, L. M., Lewinski, N. A. Cell membrane integrity cytotoxicity assays for cells dissociated from scleractinian coral Pocillopora sp. Under review in Scientific Reports

2022

• Cowen, L.J. and Putnam, H.M., 2022. Bioinformatics of Corals: Investigating Heterogeneous Omics Data from Coral Holobionts for Insight into Reef Health and Resilience. Annual Review of Biomedical Data Science, 5, 205-231
• Kumar, L., Vizgaudis, W., & Klein-Seetharaman, J. (2022). Structure-based survey of ligand binding in the human insulin receptor. British Journal of Pharmacology, 179( 14), 3512– 3528.
• Kumar L, Brenner N, Sledzieski S, Olaosebikan M, Lynn-Goin M, Berger B, Putnam H, Yang JK, Lewinski N, Singh R, Daniels N, Cowen L, Klein-Seetharaman J. (2022) Transfer of Knowledge from Model Organisms to Evolutionary Distant Non-Model Organisms: The Coral Pocillopora damicornis Membrane Signaling Receptome.PLoS ONE, in press
• Li, S., Roger, L. M., Klein-Seetharaman, J., Lewinski, N. A., Yang, J. (2022) Spatiotemporal dynamics of coral polyps on a fluidic platform>.Physical Review Applied, in press.
• Olaosebikan, M., Aranda Barrios, C., Cowen, L. and Shaer, O., 2022, April. Embodied Notes: A Cognitive Support Tool For Remote Scientific Collaboration in VR. In CHI Conference on Human Factors in Computing Systems Extended Abstracts (pp. 1-6).
• Olaosebikan, M., Aranda Barrios, C., Kolawole, B., Cowen, L. and Shaer, O., 2022, June. Identifying Cognitive and Creative Support Needs for Remote Scientific Collaboration using VR: Practices, Affordances, and Design Implications. In Creativity and Cognition (pp. 97-110).
• Roger, L. M., Russo, J., Jinkerson, R.E. , Giraldo, J-P, Lewinski, N. A. (2022) Engineered nanoceria alleviates thermally-induced oxidative stress in free-living Breviolum minutum (Symbiodiniaceae, formerly Clade B). Frontiers in Marine Sciences, DOI: 10.3389/fmars.2022.960173.
• Shpilker, P., Freeman, J., McKelvie, H., Ashey, J., Fonticella, J.-M., Putnam, H., Greenberg, J., Cowen, L., Couch, A. and Daniels N.M., MEDFORD: A human- and machine-readable metadata markup language, Database, Volume 2022, 2022, baac065,
• Link to the implementation of the medford parser: https://github.com/TuftsBCB/medford

2021

• Li, S., Roger, L.M., Kumar, L., Lewinski, N.A., Klein-Seetharaman, J., Gagnon, A., Putnam, H.M. and Yang, J., 2021. Digital image processing to detect subtle motion in stony coral. Scientific reports, 11(1), pp.1-9.
• Roger, L.M., Reich, H.G., Lawrence, E., Li, S., Vizgaudis, W., Brenner, N., Kumar, L., Klein-Seetharaman, J., Yang, J., Putnam, H.M. and Lewinski, N.A., 2021. Applying model approaches in non-model systems: A review and case study on coral cell culture.PloS one, 16(4), p.e0248953.
• Shpilker, P., MEtaData Format for Open Reef Data (MEDFORD). In: Garoufallou, E., Ovalle-Perandones, MA., Vlachidis, A. (eds) Metadata and Semantic Research. MTSR 2021. Communications in Computer and Information Science, vol 1537. Springer, Cham.
• Sledzieski, S., Singh, R., Cowen, L. and Berger, B., 2021. D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions. Cell Systems, 12(10), pp.969-982.

2020

• Olaosebikan, M., Cowen, L., Klein-Seetharaman, J., Yang, J., Lewinski, N., Shaer, O. (2020). Toward Collaborative Immersive Analytics for Coral Reef Data.Proceedings of the ACM CHI 2020 Workshop on Immersive Analytics.