Paul Sheridan

Paul Sheridan

Assistant Professor at the School of Mathematical and Computational Sciences, University of Prince Edward Island

Publications

Submitted articles

Sheridan, P., Ahmed, Z., Farooque, A. A. (2024). “A Fisher’s Exact Test interpretation of the TF-IDF Term-weighting Scheme”.

Sarria Hurtado, S., Sheridan, P. Mullen, T., Lai, U., Onodera, T., Randhawa, G. S., Farooque, A. A. (2024). “A Statistical Significance Testing Approach for Measuring Term Burstiness with Applications to Domain-specific Terminology Extraction”.

Peer reviewed journal articles

Boluwade, A., Sheridan, P., Farooque, A. A. (2024). “Spatial Modeling of Extreme Temperature in the Canadian Prairies using Max-stable Processes”. Results in Engineering, 101879. Full text available at Results in Engineering.

Sheridan, P., Onsjö, M. (2023). “The Hypergeometric Test Performs Comparably to a Common TF-IDF Variant on Standard Information Retrieval Tasks”. Multimedia Tools and Applications, 1-16. Full text available at Multimedia Tools and Applications. Preprint available at arXiv.

Yamaguchi, K., Nakagawa, S., Saku, A., Isoba, Y., Yamaguchi, R., Sheridan, P., Takane, K., Ikenoue, T., Zhu, C., Miura, M., Nagatoshi, S., Aikou, S., Shida, Y., Shida, D., Tsumoto, K., Miyano, S., Imoto, S., Furukawa, Y. (2023). “Bromodomain Protein BRD8 Regulates Cell Cycle Progression in Colorectal Cancer Cells Through a TIP-60-independent Regulation of the pre-RC Complex”. iScience, 26(4): 106563. Full text available at iScience.

Thong, P., Sheridan, P., Shimodaira, H. (2021). “Non-parametric Estimation of the Preferential Attachment Function from on Network Snapshot”. Journal of Complex Networks, 9(5): cnab024. Full text available at Journal of Complex Networks.

Thong, P., Sheridan, P., Shimodaira, H. (2020). “PAFit: An R Package for Modeling and Estimating Preferential Attachment and Node Fitness in Temporal Complex Networks”. Journal of Statistical Software, 92(3): 1-30. Full text available at Journal of Statistical Software.

Onsjö, M., Sheridan, P. (2020) “Theme Enrichment Analysis: A Statistical Test for Identifying Significantly Enriched Themes in a List of Stories with an Application to the Star Trek Television Franchise”. Digital Studies/Le champ numérique, 10(1): 1. Note: Both authors contributed equally to this work. Full text available at Digital Studies/Le champ numérique.

Sheridan, P., Onsjö, M., Becerra, C., Jimenez, S., Dueñas, G. (2019), “An Ontology-Based Recommender System with an Application to the Star Trek Television Franchise”. Future Internet, 11(9): 182. Full text available at Future Internet.

Inoue, D., Fujino, T., Sheridan, P., Zhang, Y., Nagase, R., Horikawa, S., Li, Z., Matsui, H., Kanai, A., Saika, M., Yamaguchi, R., Kozuka-Hata, H., Kawabata, K., Yokoyama, A., Goyama, S., Inaba, T., Imoto, S., Miyano, S., Xu, M., Yang, F., Oyama, M., Kitamura, T. (2018). “A Novel ASXL1-OGT Axis Plays Roles in H3K4 Methylation and Tumor Suppression in Myeloid Malignancies”. Leukemia, 32: 1327-1337. Full text available at Leukemia.

Sheridan, P., Onodera, T. (2018). “A Preferential Attachment Paradox: How Preferential Attachment Combines with Growth to Produce Networks with Log-normal In-degree Distributions”. Scientific Reports, 8: 2811. Full text available at Scientific Reports.

Lyons, E., Sheridan, P., Tremmel, G., Miyano, S., Sugano, S. (2017). “Large-scale DNA Barcode Library Generation for Biomolecule Identification in High-throughput Screens”. Scientific Reports, 7: 13899. Full text available at Scientific Reports.

Thong, P., Sheridan, P., Shimodaira, H. (2016). “Joint Estimation of Preferential Attachment and Node Fitness in Growing Networks”. Scientific Reports, 6: 32558. Full text available at Scientific Reports.

Koso, H., Yi, H., Sheridan, P., Miyano, S., Ino, Y., Todo, T., Watanabe, S. (2016). “Identification of RNA-Binding Protein LARP4B as a Tumor Suppressor in Glioma”. Cancer Research, 76: 2254-2264. Full text available at Cancer Research.

Thong, P., Sheridan, P., Shimodaira, H. (2015). “A Statistical Method for Measuring Preferential Attachment in Temporal Complex Networks”. PloS ONE, e0137796. Full text available at PloS ONE.

Takahashi, Y., Sheridan, P., Niida, A., Sawada, G., Uchi, R., Mizuno, H., Kurashige, J., Sugimachi, K., Sasaki, S., Shimada, Y., Hase, K., Kusunoki, M., Kudo, S., Watanabe, M., Yamada, K., Sugihara, K., Yamamoto, H., Suzuki, A., Doki, Y., Miyano, S., Mori, M., Mimori, K. (2015). “The AURKA/TPX2 Axis Drives Colon Tumorigenesis Cooperatively with MYC”. Annals of Oncology, 26: 935-942. Full text available at Annals of Oncology.

Balogun, E., Balogun, J., Yusuf, S., Inuwa, H., Ndams, I., Sheridan, P., Inoaka, D., Shiba, T., Harada, S., Kita, K., Esievo, K., Nok, A. (2014). “Anemia Amelioration by Lactose Infusion During Trypanosomosis could be Associated with Erythrocytes Membrane De-galactosylation”. Veterinary Parasitology, 199: 259-263. Full text available at Veterinary Parasitology.

Sheridan, P., Yagahara, Y., Shimodaira, H. (2012). “Measuring Preferential Attachment in Growing Networks with Missing-timelines using Markov Chain Monte Carlo”. Physica A, 20: 5031-5040. Full text available at Physica A.

Sheridan, P., Kamimura, T., Shimodaira, H. (2010). “A Scale-free Structure Prior for Graphical Models with Applications in Functional Genomics”. PLoS ONE, 5(11): e13580. Full text available at PLoS ONE.

Sheridan, P., Yagahara, Y., Shimodaira, H. (2008). “A Preferential Attachment Model with Poisson Growth for Scale-free Networks”. Annals of the Inustitute of Statistical Mathematics, 60: 747-761. Full text available at Annals of the Inustitute of Statistical Mathematics.

Conference activity

Papers

Lai, U., Randhawa, G. S., Sheridan, P. (2023). “Heaps’ Law in GPT-Neo Large Language Model Emulated Corpora”. Accepted at NTCIR-17, Track EVIA. Preprint available at arXiv.

Sheridan, P., Onsjö, M., Hastings, J. (2019). “The Literary Theme Ontology for Media Annotation and Information Retrieval”. Proceedings of JOWO2019: The Joint Ontology Workshops, Graz, Austria, September 23-25. Full text available at Proceedings of the Joint Ontology Workshops 2019 Episode V: The Styrian Autumn of Ontology.

Thong, P., Sheridan, P., Shimodaira, H. (2015). “Nonparametric Estimation of the Preferential Attachment Function in Complex Networks: Evidence of Deviations from Log Linearity”. Proceedings of ECCS’14: European Conference on Complex Systems, Lucca, Italy, September 22-26. Full text available at Proceedings of ECCS 2014.

Onodera, T., Sheridan, P. (2013). “Maximum Likelihood Estimation of Preferential Attachment in Growing Networks”. Proceedings of the International Workshop on Phase Transition, Critical Phenomena and Related Topics in Complex Networks, Sapporo, Japan, September 9-11.

Sheridan, P., Kamimura, T., Shimodaira, H. (2009). “On Scale-free Priors and their Applicability in Large-scale Network Inference with Graphical Models”. Complex 2009: Complex Sciences, Shanghai, China, February 23-25. Full text available at Complex 2009: Complex Sciences.

Posters

Yamaguchi, K., Nakagawa, S., Yamaguchi, R., Sheridan, P., Takane, K., Ikenoue, T., Nagatoichi, S., Kozuka-Hata, H., Oyama, M., Aikou, S., Ahiko, Y., Shida, D., Tsumoto, K., Miyano, S., Imoto, S., Furukawa, Y. (2024). “TIP60-independent Mechanism of BRD8 is involved in Colorectal Tumorigenesis”, AACR Annual Meeting, San Diego, USA, April 4-10.

Sheridan, P., Tremmel, G., Yamaguchi, R., Imoto, S., Miyano, S. (2015). “Headache-free Geneset Analysis for the Working Molecular Biologist”. 42nd IMSUT Founding Commemorative Symposium, Tokyo, Japan, June 1-2.

Takahashi, Y., Sheridan, P., Niida, A., Sawada, G., Uchi, R., Mizuno, H., Kurashige, J., Sugimachi, K., Sasaki, S., Shimada, Y., Hase, K., Kusunoki, M., Kudo, S., Watanabe, M., Yamada, K., Sugihara, K., Yanamoto, H., Suzuki, A., Doki, Y., Miyano, S., Mori, M., Mimori, K. (2013). “Genomic Co-amplification of TPX2 and AURKA with MYC Cooperatively Promote MYC-driven Carcinogenesis”. Systems Cancer Workshop, Tokyo, Japan, December.

Sheridan, P., Onodera, T. (2013). “The Resolution of a Minor Preferential Attachment Paradox makes Major Confusions Plain”. The International Workshop on Phase Transition, Critical Phenomena and Related Topics in Complex Networks, Sapporo, Japan, September 9-11.

Sheridan, P., Yagahara, Y., Shimodaira, H. (2009). “Estimating Preferential Attachment in Growing Networks with Unknown Node Ordering”. Global COE Opening Symposium, Tokyo, Japan, January 30 - February 1.

Sheridan, P., Kamimura, T., Shimodaira, H. (2008). “Estimating Gene Networks from Microarray Data using Graphical Models with Scale-free Priors”. Pacific Symposium on Biocomputing, Big Island of Hawaii, USA, January 4-8.

Sheridan, P., Kamimura, T., Shimodaira, H. (2007). “Comparing Scale-free Priors over Graph Structures for Bayesian Inference of Gene Networks”. Pacific Symposium on Biocomputing, Maui, USA, January 3-7.