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Zhao, L., Arnett, C. M., Casey, V. I., Scott, J. W., Davis, M. A., Heidkamp, G., & Wilson, R. C. (2025). Profiling Specific Volatile Organic Compounds for Mold Detection and Species Identification. Indoor Air, 2025(1), Article 9350601. https://doi.org/10.1155/ina/9350601
Warnow, T., Tabatabaee, Y., & Evans, S. N. (2025). Advances in Estimating Level-1 Phylogenetic Networks from Unrooted SNPs. Journal of computational biology : a journal of computational molecular cell biology, 32(1), 3-27. https://doi.org/10.1089/cmb.2024.0710
Vu-Le, T. A., Anne, L., Chacko, G., & Warnow, T. (2025). EC-SBM synthetic network generator. Applied Network Science, 10(1), Article 15. https://doi.org/10.1007/s41109-025-00701-2
Vu-Le, T. A., Park, M., Chen, I., & Warnow, T. (2026). Using stochastic block models for community detection. Applied Network Science, 11(1), Article 2. Advance online publication. https://doi.org/10.1007/s41109-025-00747-2
Vora, M., Shomorony, I., & Ornik, M. (2025). Capacity-Aware Planning and Scheduling in Budget-Constrained Multi-Agent MDPs: A Meta-RL Approach. IEEE Robotics and Automation Letters, 10(11), 11944-11951. https://doi.org/10.1109/LRA.2025.3617726
Tebele, S. M., Marks, R. A., & Farrant, J. M. (2025). Microbial survival strategies in desiccated roots of Myrothamnus flabellifolia. Frontiers in Microbiology, 16, Article 1560114. https://doi.org/10.3389/fmicb.2025.1560114
Taylor, W., & O’Dwyer, J. (2025). On the structure of multiple stable equilibria in competitive ecological systems. Theoretical Ecology, 18(1), Article 31. https://doi.org/10.1007/s12080-025-00627-6
Tabatabaee, Y., Wedell, E., Park, M., & Warnow, T. (2025). FastEnsemble: A New Scalable Ensemble Clustering Method. In H. Cherifi, M. Donduran, L. M. Rocha, C. Cherifi, & O. Varol (Eds.), Complex Networks and Their Applications XIII - Proceedings of The 13th International Conference on Complex Networks and Their Applications: COMPLEX NETWORKS 2024 - Volume 3 (pp. 57-70). (Studies in Computational Intelligence; Vol. 1189 SCI). Springer. https://doi.org/10.1007/978-3-031-82435-7_5
Tabatabaee, Y., Wedell, E., Park, M., & Warnow, T. (2025). FastEnsemble: Scalable ensemble clustering on large networks. PLOS Complex Systems, 2(10 October), Article e0000069. https://doi.org/10.1371/journal.pcsy.0000069
Shin, S., Shomorony, I., & Macgregor, P. (2025). Dynamic DBSCAN with Euler Tour Sequences. Proceedings of Machine Learning Research, 258, 1495-1503.
Shen, C., Wedell, E., Pop, M., & Warnow, T. (2025). TIPP3 and TIPP3-fast: Improved abundance profiling in metagenomics. PLoS computational biology, 21(4), Article e1012593. https://doi.org/10.1371/journal.pcbi.1012593
Sharaf, A., Marks, R., & Khayi, S. (2025). Advances in telomere-to-telomere plant genomes. In Plant Pangenomes and Pangenomics (pp. 571-592). Elsevier. https://doi.org/10.1016/B978-0-443-26791-8.00027-3
Samuels, L. R. N., Chandler, H. C., Hoffman, M., Kronenberger, J. A., Elmore, M., Aldredge, R., Stegenga, B. S., Bogan, J. E., Davis, M. A., Hertz, S., Schwartz, M. K., & Wilcox, T. (2025). Persistence of Reptile DNA in a Terrestrial Substrate: A Case Study Using the Eastern Indigo Snake. Environmental DNA, 7(1), Article e70053. https://doi.org/10.1002/edn3.70053
Samuels, L. R. N., Wilcox, T., Hoffman, M., Elmore, M., Aldredge, R., Stegenga, B. S., Bogan, J. E., Davis, M. A., Hertz, S., Schwartz, M. K., & Chandler, H. C. (2025). Comparison of camera traps, eDNA, and visual encounter surveys for threatened species detection. Journal for Nature Conservation, 86, Article 126948. https://doi.org/10.1016/j.jnc.2025.126948
Reves, O. P., Davis, M. A., Iacaruso, N. J., & Larson, E. R. (2025). Environmental DNA quantifies the terrestrial biodiversity co-benefit of forested riparian buffers in agricultural landscapes. Journal of Applied Ecology, 62(12), 3469-3479. https://doi.org/10.1111/1365-2664.70206
Pop, M., Attwood, T. K., Blake, J. A., Bourne, P. E., Conesa, A., Gaasterland, T., Hunter, L., Kingsford, C., Kohlbacher, O., Lengauer, T., Markel, S., Moreau, Y., Noble, W. S., Orengo, C., Ouellette, B. F. F., Parida, L., Przulj, N., Przytycka, T. M., Ranganathan, S., ... Warnow, T. (2025). Biological databases in the age of generative artificial intelligence. Bioinformatics Advances, 5(1), Article vbaf044. https://doi.org/10.1093/bioadv/vbaf044
Park, M., Feng, D. W., Digra, S., Vu-Le, T. A., Chacko, G., & Warnow, T. (2025). Improved Community Detection Using Stochastic Block Models. In H. Cherifi, M. Donduran, L. M. Rocha, C. Cherifi, & O. Varol (Eds.), Complex Networks and Their Applications XIII - Proceedings of The 13th International Conference on Complex Networks and Their Applications: COMPLEX NETWORKS 2024 - Volume 3 (pp. 103-114). (Studies in Computational Intelligence; Vol. 1189 SCI). Springer. https://doi.org/10.1007/978-3-031-82435-7_9
O’Dwyer, J. P., Lutz, J. A., Schappe, T., Alegre, D., Black, A. N., Grünwald, N. J., & Jones, F. A. (2025). Genomic demography predicts community dynamics in a temperate montane forest. Science, 389(6766), Article eadu6396. https://doi.org/10.1126/science.adu6396
Mazooji, K., & Shomorony, I. (2025). Guaranteed Recovery of Unambiguous Clusters. In ISIT 2025 - 2025 IEEE International Symposium on Information Theory, Proceedings (IEEE International Symposium on Information Theory - Proceedings). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISIT63088.2025.11195317
Marks, R. A., Ekwealor, J. T. B., Artur, M. A. S., Bondi, L., Boothby, T. C., Carmo, O. M. S., Centeno, D. C., Coe, K. K., Dace, H. J. W., Field, S., Hutt, A., Porembski, S., Thalhammer, A., van der Pas, L., Wood, A. J., Alpert, P., Bartels, D., Boeynaems, S., Datar, M. N., ... Rhee, S. Y. (2025). Life on the dry side: a roadmap to understanding desiccation tolerance and accelerating translational applications. Nature communications, 16(1), Article 3284. https://doi.org/10.1038/s41467-025-58656-y
Li, Y. H., Sima, J., Shomorony, I., & Milenkovic, O. (2025). Reducing Fragmentation in Data Deduplication Systems via Partial Repetition and Coding. IEEE Transactions on Information Theory, 71(11), 8324-8345. https://doi.org/10.1109/TIT.2025.3613455
Li, Y. H., Sima, J., Shomorony, I., & Milenkovic, O. (2025). Fragmentation in Data Deduplication Systems I: The Stretch Metric. In ISIT 2025 - 2025 IEEE International Symposium on Information Theory, Proceedings (IEEE International Symposium on Information Theory - Proceedings). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISIT63088.2025.11195219
Li, Y. H., Sima, J., Shomorony, I., & Milenkovic, O. (2025). Fragmentation in Data Deduplication Systems II: The Jump Metric. In ISIT 2025 - 2025 IEEE International Symposium on Information Theory, Proceedings (IEEE International Symposium on Information Theory - Proceedings). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISIT63088.2025.11195582
Laserna, A. V., Phillips, C. A., Kuhns, A. R., Davis, M. A., Corush, J. B., & Paige, K. N. (2025). Spatio-Temporal Patterns of Hybridization in an Alloploid Salamander (Ambystomatidae: Ambystoma) and Conservation Implications of Introgression in a Unisexual Vertebrate. Ecology and Evolution, 15(1), Article e70765. https://doi.org/10.1002/ece3.70765
Karimi, P., Shomorony, I., Zhao, Z., & Kamalabadi, F. (2025). Aggregated Kalman Filter: Efficient Switching Linear Dynamic Estimation via Merging Priors. IEEE Transactions on Signal Processing, 73, 4415-4429. https://doi.org/10.1109/TSP.2025.3612347
Jops, K., Dalling, J. W., & O’Dwyer, J. P. (2025). Life history is a key driver of temporal fluctuations in tropical tree abundances. Proceedings of the National Academy of Sciences of the United States of America, 122(4), Article e2422348122. https://doi.org/10.1073/pnas.2422348122
Johnson, M. D., Tetzlaff, S. J., Katz, A. D., Tiemann, J., Smith, C., Dana, C. E., Pearce, S. E., Davis, M. A., Hartman, J. H., & Sperry, J. H. (2025). Environmental DNA Metabarcoding Elucidates Freshwater Mussel Diversity and Occupancy to Facilitate Improved Management and Conservation. Diversity and Distributions, 31(3), Article e70008. https://doi.org/10.1111/ddi.70008
Gerzon, Y., Shomorony, I., & Weinberger, N. (2025). Capacity of Frequency-Based Channels: Encoding Information in Molecular Concentrations. IEEE Transactions on Information Theory, 71(8), 5788-5808. https://doi.org/10.1109/TIT.2025.3578504
Douglass, S. A., Palmer, S., McCallum, A. R., Reves, O. P., Robinson, H. A., Rutledge, A. J., Hartman, J. H., Larson, E. R., & Davis, M. A. (2025). Environmental DNA reveals the Salamander Mussel Simpsonaias ambigua alive in Illinois, USA, after a century in obscurity. Ecology, 106(7), Article e70145. https://doi.org/10.1002/ecy.70145
Corush, J. B., Cucalón, R. V., Metzke, B. A., Tan, M., & Davis, M. A. (2025). Pleistocene glaciation and Anthropocene fragmentation influence genetic variation in the Illinois state–listed mottled sculpin (Cottus bairdii). Environmental Biology of Fishes, 108(6), 905-922. https://doi.org/10.1007/s10641-025-01686-8
Butler, S. E., Iacaruso, N. J., Davis, M. A., Woiak, Z., & Parkos, J. J. (2025). Assessing the efficacy of a quantitative PCR screening procedure for detecting and quantifying the magnitude of invasive carp reproductive events. North American Journal of Fisheries Management, 45(5), 851-866. https://doi.org/10.1093/najfmt/vqaf066
Arya, S., George, A. B., & O'Dwyer, J. (2025). The architecture of theory and data in microbiome design: towards an S-matrix for microbiomes. Current Opinion in Microbiology, 83, Article 102580. https://doi.org/10.1016/j.mib.2025.102580
Anne, L., Vu-Le, T. A., Park, M., Warnow, T., & Chacko, G. (2025). Synthetic Networks That Preserve Edge Connectivity. In H. Cherifi, M. Donduran, L. M. Rocha, C. Cherifi, & O. Varol (Eds.), Complex Networks and Their Applications XIII - Proceedings of The 13th International Conference on Complex Networks and Their Applications: COMPLEX NETWORKS 2024 - Volume 3 (pp. 166-177). (Studies in Computational Intelligence; Vol. 1189 SCI). Springer. https://doi.org/10.1007/978-3-031-82435-7_14
Anne, L., Vu-Le, T. A., Park, M., Warnow, T., & Chacko, G. (2025). RECCS: REALISTIC CLUSTER CONNECTIVITY SIMULATOR FOR SYNTHETIC NETWORK GENERATION. Advances in Complex Systems, 28(5), Article 2540004. https://doi.org/10.1142/S0219525925400041