Recent Scientific Publications

As of May 19, 2025

Hopkinson, C., Weston, N., Vallino, J., Garritt, R., & Forbrich, I. (2025). Comparative Metabolism and Blue Carbon Sequestration of Two Wetland-Dominated Estuaries. Ocean-Land-Atmosphere Research, 0091. https://doi.org/10.34133/olar.0091

Irvine, T., Costello, J. H., Gemmell, B. J., Sutherland, K. R., Corrales-Ugalde, M., Townsend, J. P., & Colin, S. P. (2025). Ctenophores are a highly impactful predatory guild in open oceanic ecosystems. Current Biology. https://doi.org/10.1016/j.cub.2025.04.029

Qian, G., Zhang, H., Liu, Y., Shribak, M., Eliceiri, K. W., & Provenzano, P. P. (2025). Computationally Enabled Polychromatic Polarized Imaging Enables Mapping of Matrix Architectures that Promote Pancreatic Ductal Adenocarcinoma Dissemination. The American Journal of Pathology. https://doi.org/10.1016/j.ajpath.2025.04.017

Tucker, S. J., Rii, Y. M., Freel, K. C., Kotubetey, K., Kawelo, A. H., Winter, K. B., & Rappe, M. S. (2025). Seasonal and spatial transitions in phytoplankton assemblages spanning estuarine to open ocean waters of the tropical Pacific. Limnology and Oceanography. https://doi.org/10.1002/lno.70075

Walker, S. E., Yu, K., Burgess, S., & Echeverri, K. (2025). Neuronal activation in the axolotl brain promotes tail regeneration. npj Regenerative Medicine, 10, 22. https://doi.org/10.1038/s41536-025-00413-2

Yoshino, J., Mali, S. S., Williams, C. R., Morita, T., Emerson, C. E., Arp, C. J., Miller, S. E., Yin, C., Thé, L., Hemmi, C., Motoyoshi, M., Ishii, K., Emoto, K., Bautista, D. M., & Parrish, J. Z. (2025). Drosophila epidermal cells are intrinsically mechanosensitive and modulate nociceptive behavioral outputs. eLife, 13, RP95379. https://doi.org/10.7554/eLife.95379

Liu, J., Costello, J., & Kanso, E. (2025). Flow physics of nutrient transport drives functional design of ciliates. Nature Communications, 16, 4154. https://doi.org/10.1038/s41467-025-59413-x

Boudreau, V., Albright, A. R., Larson, B. T., Gerbich, T. M., Fadero, T., Yan, V., Lucas-DeMott, A., Yung, J., Moulin, S. L. Y., Descovich, C. P., Slabodnick, M. M., Burlacot, A., Wang, J. R., Niyogi, K. K., & Marshall, W. F. (2025). The cell biology and genome of Stentor pyriformis, a giant cell that embeds symbiotic algae in a microtubule meshwork. Molecular Biology of the Cell, 36(4). https://doi.org/10.1091/mbc.E24-12-0571

Chitsaz, M., Yang, L., Rayes-Danan, R., Savari, O., Li, B., Shribak, M., Eliceiri, K., & Loeffler, A. (2025). Polychromatic Polarization Microscopy Differentiates Collagen Fiber Signatures in Benign Pancreatic Tissue and Pancreatic Ductal Adenocarcinoma. Modern Pathology, 100768. https://doi.org/10.1016/j.modpat.2025.100768

Stekoll, M., Lindell, S., Goudey, C. A., Kite-Powell, H. L., Bailey, D., Barbery, K., Roberson, L., Peeples, T., Mangini, N., Pryor, A., Meyer, A., & Yarish, C. (2025). Development of scalable coastal and offshore kelp farming for marine biomass production. Journal of the World Aquaculture Society, 56(2), e70017. https://doi.org/10.1111/jwas.70017

Vargas, K. J., Wallace, J. N., Mooney, I., Owen, D. J., & Morgan, J. R. (2025). α-Synuclein interacts directly with AP2 and regulates its binding to synaptic membranes. Journal of Biological Chemistry, 108502. https://doi.org/10.1016/j.jbc.2025.108502

Giacomini, J. J., Torres-Morales, J., Dewhirst, F. E., Borisy, G. G., & Mark Welch, J. L. (2025). Spatial ecology of the Neisseriaceae family in the human oral cavity. Microbiology Spectrum, e03275-24. https://doi.org/10.1128/spectrum.03275-24

Henthorn, D., Wilson, S., Tank, R. K., Mallard, W., Fadero, T., Gao, R., & Garner, E. C. (2025). Bacillus subtilis twisting arises from torsional stress established by cell wall insertion and released by hydrolase-mediated cell wall cleavage. Molecular Biology of the Cell, 36(5), ar56. https://doi.org/10.1091/mbc.E24-09-0396

Sebastian, H., Robador, A., Ray, D., Angermeyer, A., D’Hondt, S., Huber, J. A., & Finkel, S. E. (2025). Identifying potential nutrient acquisition mechanisms for long-term survival: Adaptive evolution of Halomonas isolated from subseafloor crustal fluids. Frontiers in Microbiology, 16, 1511421. https://doi.org/10.3389/fmicb.2025.1511421

Shekhar, S., Guo, H., Colin, S. P., Marshall, W., Kanso, E., & Costello, J. H. (2025). Cooperative hydrodynamics accompany multicellular-like colonial organization in the unicellular ciliate Stentor. Nature Physics. https://doi.org/10.1038/s41567-025-02787-y

Kananen, K., Veseli, I., Quiles Pérez, C., Miller, S., Eren, A., & Bradley, P. (2025). Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes. Bioinformatics Advances, 5(1), vbaf039. https://doi.org/10.1093/bioadv/vbaf039

Valiela, I., Chenoweth, K., & Day, J. (2025). Meta-analysis of vegetation responses to experimental nitrogen enrichments done in salt marshes under different sea level rise regimes reveal interaction of N supply and sea level rise. Science of The Total Environment, 975, 179198. https://doi.org/10.1016/j.scitotenv.2025.179198

Zottoli, S. J., Kaczmarek, L. K., & Faber, D. S. (2025). Multiple Neuronal Processes, Including the Mauthner Axon, Form a Multi-Axial Fiber Within a Common Myelin Sheath in the Central Nervous System of Adult Lungfishes, Protopterus annectens, Lepidosiren paradoxa, and Neoceratodus forsteri. Journal of Morphology, 286(4), e70042. https://doi.org/10.1002/jmor.70042

Griffin, C., Coppenrath, K., Khan, D., Lin, Z., Horb, M., & Saint-Jeannet, J.-P. (2025). Deletion of sf3b4 causes splicing defects and gene dysregulation that disrupt craniofacial development and survival. Disease Models & Mechanisms, 18(3). https://doi.org/10.1242/dmm.052169

Liu, J., Burkart, T., Ziepke, A., Reinhard, J., Chao, Y.-C., Tan, T. H., Swartz, S. Z., Frey, E., & Fakhri, N. (2025). Light-induced cortical excitability reveals programmable shape dynamics in starfish oocytes. Nature Physics, 1–10. https://doi.org/10.1038/s41567-025-02807-x

Ribeiro, R., Null, R., & Özpolat, B. (2025). Sex-biased gene expression precedes sexual dimorphism in the agonadal annelid Platynereis dumerilii. Development. https://doi.org/10.1242/dev.204513

Simon, S., Soares, A., Bornemann, T., Lange, A., Griesdorn, L., Fuentes, A., Dieckmann, M., Krok, B., Ruff, S., Hügler, M., Moraru, C., & Probst, A. (2025). Inferring replication states of bacteria and viruses in enrichment cultures via long-read sequencing. ISME Communications, ycaf041. https://doi.org/10.1093/ismeco/ycaf041

Loh, L., DeMarr, K., Tsimba, M., Heryanto, C., Berrio, A., Patel, N., Martin, A., McMillan, W., Wray, G., & Hanly, J. (2025). Lepidopteran scale cells derive from sensory organ precursors through a canonical lineage. Development, 152(5).https://doi.org/10.1242/dev.204501

Pedrosa-Pamies, R., Conte, M. H., Weber, J. C., & Andersson, A. J. (2025). Hurricane-driven transport of bermuda reef carbonate platform sediments to the deep ocean. Journal of Geophysical Research: Oceans, 130(3), e2023JC020500.https://doi.org/10.1029/2023JC020500

Stegen, J., Burgin, A., Busch, M., Fisher, J., Ladau, J., Abrahamson, J., Kinsman-Costello, L., Li, L., Chen, X., Datry, T., McDowell, N., Tatariw, C., Braswell, A., Deines, J., Guimond, J., Regier, P., Rod, K., Bam, E., Fluet-Chouinard, E., Forbrich, I., … Patel, K. (2025). Reviews and syntheses: Variable inundation across Earth’s terrestrial ecosystems. Biogeosciences, 22(4), 995–1034.https://doi.org/10.5194/bg-22-995-2025

Conte, M., Pedrosa-Pamies, R., Weber, J., & Johnson, R. (2025). The climatology of the deep particle flux in the oligotrophic western North Atlantic gyre, 1978–2022. Progress In Oceanography, 103433.https://doi.org/10.1016/j.pocean.2025.103433

Damian-Serrano, A., Walton, K., Bishop-Perdue, A., Bagoye, S., Du Clos, K., Gemmell, B., Colin, S., Costello, J., & Sutherland, K. (2025). Colonial architecture modulates the speed and efficiency of multi-jet swimming in salp colonies. Journal of Experimental Biology.https://doi.org/10.1242/jeb.249465

Hoffmann, C., Ruff, K., Edu, I., Shinn, M., Tromm, J., King, M., Pant, A., Ausserwöger, H., Morgan, J., Knowles, T., Pappu, R., & Milovanovic, D. (2025). Synapsin condensation is governed by sequence-encoded molecular grammars. Journal of Molecular Biology, 168987.https://doi.org/10.1016/j.jmb.2025.168987

Hoffmann, C., Ruff, K., Edu, I., Shinn, M., Tromm, J., Pant, A., Ausserwöger, H., Morgan, J., Knowles, T., Pappu, R., & Milovanovic, D. (2025). BPS2025—Sequence-encoded molecular grammar governs the formation of synaptic condensates. Biophysical Journal, 124(3), 562a.https://doi.org/10.1016/j.bpj.2024.11.2925

Jiang, Q., Cao, L., Han, Y., Li, S., Zhao, R., Zhang, X., Ruff, S., Zhao, Z., Peng, J., Liao, J., Zhu, B., Wang, M., Lin, X., & Dong, X. (2025). Cold seeps are potential hotspots of deep-sea nitrogen loss driven by microorganisms across 21 phyla. Nature Communications, 16(1), 1646.https://doi.org/10.1038/s41467-025-56774-1

Martinez, A., Hall, L., Fuentes, M., Putland, R., & Mensinger, A. (2025). The effects on anthropogenic sound on embryonic little skates (Leucoraja erinacea) and chain dogfish (Scyliorhinus rotifer). Journal of Experimental Biology.https://doi.org/10.1242/jeb.249394

Sullivan, H. L., Holtzer, J., Deegan, L. A., & Bowen, J. L. (2025). The Effect of runnels on salt marsh sediment dynamics, vegetation, and nitrogen cycling. Estuaries and Coasts, 48(3), 73.https://doi.org/10.1007/s12237-025-01511-6

Guimond, J., Grande, E., Michael, H., Pratt, D., Herndon, E., Noyce, G., Ward, N., Forbrich, I., Regier, P., Berens, M., & Arora, B. (2025). The hidden influence of terrestrial groundwater on salt marsh function and resilience. Nature Water, 1–10.https://doi.org/10.1038/s44221-024-00384-6

Martens, K., de Almeida, N. M., Shribak, M., Higuti, J., & Schön, I. (2025). On Cytheridella whitmani sp. Nov. (Crustacea, Ostracoda) from Cape Cod (Massachusetts, USA), with a reappraisal of the taxonomy of the genus. ZooKeys, 1224, 317–348.https://doi.org/10.3897/zookeys.1224.135458

Sow, S. L. S., van de Poll, W. H., Eveleth, R., Rich, J. J., Ducklow, H. W., Rozema, P. D., Luria, C. M., Bolhuis, H., Meredith, M. P., Amaral-Zettler, L. A., & Engelmann, J. C. (2025). Spatial and temporal variation of Antarctic microbial interactions: A study around the west Antarctic Peninsula. Environmental Microbiome, 20(1), 21.https://doi.org/10.1186/s40793-025-00663-z

McCoy, D. E., Burns, D. H., Klopfer, E., Herndon, L. K., Ogunlade, B., Dionne, J. A., & Johnsen, S. (2024). Heart cockle shells transmit sunlight to photosymbiotic algae using bundled fiber optic cables and condensing lenses. Nature Communications, 15(1), 9445.https://doi.org/10.1038/s41467-024-53110-x

 Zhao, Y., Zhou, R., Xie, B., Liu, C., Kalski, M., Cham, C., Jiang, Z., Koval, J., Weber, C., Rubin, D., Sogin, M., Crosson, S., Chen, M., Huang, J., Fiebig, A., Dalal, S., Chang, E., Basu, A., & Pott, S. (2025). Multiomic analysis reveals cellular, transcriptomic and epigenetic changes in intestinal pouches of ulcerative colitis patients. Nature Communications, 16(1), 904.https://doi.org/10.1038/s41467-025-56212-2

MacCord, K. (2025). Let’s talk about sex…cell lineages. Biological Theory, 1–14.https://doi.org/10.1007/s13752-024-00488-y

Thiruppathy, M., Teubner, L., Roberts, R., Lasser, M., Moscatello, A., Chen, Y.-W., Hochstim, C., Ruffins, S., Sarkar, A., Tassey, J., Evseenko, D., Lozito, T., Willsey, H., Gillis, J., & Crump, J. (2025). Repurposing of a gill gene regulatory program for outer ear evolution. Nature, 1–3.https://doi.org/10.1038/s41586-024-08577-5

Jimenez, V., Sudek, S., Eckmann, C., Bachy, C., Poirier, C., Wittmers, F., Santoro, A. E., Follows, M. J., Chavez, F. P., Shilova, I., & Worden, A. Z. (2024). Distinct phytoplankton assemblages underlie hotspots of primary production in the eastern North Pacific Ocean. Limnology and Oceanography.https://doi.org/10.1002/lno.12771

Liu, J., Man, Y., Costello, J. H., & Kanso, E. (2025). Optimal feeding in swimming and attached ciliates. Journal of Fluid Mechanics, 1003, A26.https://doi.org/10.1017/jfm.2024.1139

Longman, E. K., Merolla, S., Talke, S. A., Trautman, N., Largier, J. L., Harris, L., & Sanford, E. (2025). Evaluating historical changes in a mussel bed community in northern California. Scientific Reports, 15(1), 1930.https://doi.org/10.1038/s41598-025-86105-9

Handa, S., Biswas, T., Chakraborty, J., Ghosh, G., Paul, B. G., & Ghosh, P. (2025a). RNA control of reverse transcription in a diversity-generating retroelement. Nature.https://doi.org/10.1038/s41586-024-08405-w

Handa, S., Biswas, T., Chakraborty, J., Ghosh, G., Paul, B., & Ghosh, P. (2025b). RNA control of reverse transcription in a diversity-generating retroelement. Nature.https://doi.org/10.1038/s41586-024-08405-w

Hinkle, J., Chanton, J., Moynihan, M., Ruff, S., & Teske, A. (2025). Complex bacterial diversity of Guaymas Basin hydrothermal sediments revealed by synthetic long-read sequencing (LoopSeq). Frontiers in Microbiology, 15, 1491488.https://doi.org/10.3389/fmicb.2024.1491488

Peredo, E., Thomas, S., & Cardon, Z. (2025). Draft genome sequence of Mycobacterium sp. SA01 isolated from Sporobolus alterniflorus seedlings collected in Cape Cod (USA). Microbiology Resource Announcements, e0102524.https://doi.org/10.1128/mra.01025-24

Troman, L., de Gaulejac, E., Biswas, A., Stiens, J., Kuropka, B., Moores, C. A., & Reber, S. (2025). Mechanistic basis of temperature adaptation in microtubule dynamics across frog species. Current Biology.https://doi.org/10.1016/j.cub.2024.12.022

Almoril-Porras, A., Calvo, A., Niu, L., Beagan, J., Díaz García, M., Hawk, J., Aljobeh, A., Wisdom, E., Ren, I., Wang, Z.-W., & Colón-Ramos, D. (2024). Configuration of electrical synapses filters sensory information to drive behavioral choices. Cell.https://doi.org/10.1016/j.cell.2024.11.037

Bower, D., Senft, S., Hanlon, R., & Deravi, L. (2024). Pigment granule architecture varies across yellow, red, and brown chromatophores in squid Doryteuthis pealeii. Scientific Reports, 14(1), 31417.https://doi.org/10.1038/s41598-024-83021-2

Hernandez-Rodriguez, Y., Bullard, A. M., Busch, R. J., Marshall, A., & Vargas-Muñiz, J. M. (2024). Strategies for genetic manipulation of the halotolerant black yeast Hortaea werneckii: Ectopic DNA integration and marker-free CRISPR/Cas9 transformation. Microbiology Spectrum, 13(1), e02430-24.https://doi.org/10.1128/spectrum.02430-24 

Arkhipova, I., Burns, K., & Lesage, P. (2024). Controlling and controlled elements: Highlights of the year in mobile DNA research. Mobile DNA, 15(1), 27.https://doi.org/10.1186/s13100-024-00340-x

Arrington, E., Tarn, J., Kivenson, V., Nunn, B., Liu, R., Paul, B., & Valentine, D. (2024). Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus. The ISME Journal: Multidisciplinary Journal of Microbial Ecology, wrae247.https://doi.org/10.1093/ismejo/wrae247

 Evans, B., Gvozdik, V., Knytl, M., Cauret, C., Herrel, A., Greenbaum, E., Patel, J., Premachandra, T., Papenfuss, T., Parente, J., Horb, M., & Measey, J. (2024). Rapid Sex Chromosome Turnover in African Clawed Frogs (Xenopus) and the Origins of New Sex Chromosomes. Molecular Biology and Evolution, 41(12).https://doi.org/10.1093/molbev/msae234

Guo, M., Wu, Y., Hobson, C., Su, Y., Qian, S., Krueger, E., Christensen, R., Kroeschell, G., Bui, J., Chaw, M., Zhang, L., Liu, J., Hou, X., Han, X., Lu, Z., Ma, X., Zhovmer, A., Combs, C., Moyle, M., Riviere, P., Colon-Ramos, D., … Shroff, H. (2025). Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopy. Nature Communications, 16(1), 313.https://doi.org/10.1038/s41467-024-55267-x

Ruff, S., de Angelis, I., Mullis, M., Payet, J., Magnabosco, C., Lloyd, K., Sheik, C., Steen, A., Shipunova, A., Morozov, A., Reese, B., Bradley, J., Lemonnier, C., Schrenk, M., Joye, S., Huber, J., Probst, A., Morrison, H., Sogin, M., … Colwell, F. (2024). A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide. Science Advances, 10(51).https://doi.org/10.1126/sciadv.adq0645