Recent Scientific Publications

As of March 31, 2025

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 & Mechanisms18(3).

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.

Ribeiro, R., Null, R., & Özpolat, B. (2025). Sex-biased gene expression precedes sexual dimorphism in the agonadal annelid Platynereis dumerilii. Development.

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.

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. Development152(5).

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: Oceans130(3), e2023JC020500.

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. Biogeosciences22(4), 995–1034.

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.

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.

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.

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 Journal124(3), 562a.

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 Communications16(1), 1646.

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.

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 Coasts48(3), 73.

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.

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. ZooKeys1224, 317–348.

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 Microbiome20(1), 21.

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 Communications15(1), 9445.

 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 Communications16(1), 904.

MacCord, K. (2025). Let’s talk about sex…cell lineages. Biological Theory, 1–14.

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.

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.

Liu, J., Man, Y., Costello, J. H., & Kanso, E. (2025). Optimal feeding in swimming and attached ciliates. Journal of Fluid Mechanics1003, A26.

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 Reports15(1), 1930.

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.

Handa, S., Biswas, T., Chakraborty, J., Ghosh, G., Paul, B., & Ghosh, P. (2025b). RNA control of reverse transcription in a diversity-generating retroelement. Nature.

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 Microbiology15, 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.

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.

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.

Bower, D., Senft, S., Hanlon, R., & Deravi, L. (2024). Pigment granule architecture varies across yellow, red, and brown chromatophores in squid Doryteuthis pealeii. Scientific Reports14(1), 31417.

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 Spectrum13(1), e02430-24. 

Arkhipova, I., Burns, K., & Lesage, P. (2024). Controlling and controlled elements: Highlights of the year in mobile DNA research. Mobile DNA15(1), 27.

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.

 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 Evolution41(12).

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 Communications16(1), 313.

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 Advances10(51).

Griswold, J. M., Bonilla-Quintana, M., Pepper, R., Lee, C. T., Raychaudhuri, S., Ma, S., Gan, Q., Syed, S., Zhu, C., Bell, M., Suga, M., Yamaguchi, Y., Chereau, R., Valentin Naegerl, U., Knott, G., Rangamani, P., & Watanabe, S. (2024). Membrane mechanics dictate axonal pearls-on-a-string morphology and function. Nature Neuroscience. 

Hernandez, C., van Daalen, S., Liguori, A., Neubert, M., Caswell, H., & Gribble, K. (2024). Maternal effect senescence and caloric restriction interact to affect fitness through changes in life history timing. Journal of Animal Ecology.

Houghton, R., Davidson, E., Melillo, J., Schlesinger, W., & Shaver, G. (2024). Resolution of Respect: George M. Woodwell (1928–2024). Bulletin of the Ecological Society of America.

Wittmers, F., Comstock, J., Poirier, C., Needham, D. M., Schulz, F., Malmstrom, R., Carlson, C. A., & Worden, A. Z. (2024). Non-photosynthetic lineages sibling to Cyanobacteria associate with eukaryotes in the open ocean. Current Biology34(22), R1133–R1134.

Demir, C., McClelland, J., Bristol, E., Charette, M., & Cardenas, M. (2024). Coastal Supra‐Permafrost Aquifers of the Arctic and their significant groundwater, carbon, and nitrogen fluxes. Geophysical Research Letters51(22), e2024gl109142.

Gherca, W., Forbrich, I., Jacotot, A., Knox, S., Leahy, P., Morrison, R., Sachs, T., & Eichelmann, E. (2025). Biometeorological feedbacks on peatlands: Raising the water table to reduce meteorologically-related stress on cattle. Agricultural and Forest Meteorology360, 110279.

Román‐Vendrell, C., Wallace, J., Watson, A., Celikag, M., Bartels, T., & Morgan, J. (2024). Acute introduction of monomeric or multimeric α‐synuclein induces distinct impacts on synaptic vesicle trafficking at lamprey giant synapses. The Journal of Physiology.

Buschbaum, C., Shama, L. N. S., Amorim, F. L. L., Brand, S., Broquard, C. M. A., Camillini, N., Cornelius, A., Dolch, T., Dummermuth, A., Feldner, J., Guignard, M. S., Habedank, J., Hoffmann, J. J. L., Horn, S., Konyssova, G., Koop-Jakobsen, K., Lauerburg, R., Mehler, K., Odongo, V., Petri, M., Reents, S., Rick, J. J., Rubinetti, S., Salahi, M., Sander, L., Sidorenko, V., Spence-Jones, H. C., van Beusekom, J. E. E., Waser, A. M., Wegner, K. M., & Wiltshire, K. H. (2024). Climate change impacts on a sedimentary coast—A regional synthesis from genes to ecosystems. Marine Biodiversity54(4), 64.

Dames, N. R., Rocke, E., Pitcher, G., Rybicki, E., Pfaff, M., & Moloney, C. L. (2024). Ecological roles of nano-picoplankton in stratified waters of an embayment in the southern Benguela. FEMS Microbiology Letters, fnae094.

Haviland, K., Howarth, R.Giblin, A., & Marino, R. (2024). The potential role of sediment iron and sulfur speciation in seagrass meadow loss and recovery. Ocean-Land-Atmosphere Research, 3, 0069.

Iuffrida, L., Spezzano, R., Trapella, G., Cinti, N., Parma, L., De Marco, A., Palladino, G., Bonaldo, A., Candela, M., & Franzellitti, S. (2024). Physiological plasticity and life history traits affect Chamelea gallina acclimatory responses during a marine heatwave. Environmental Research263(Part 3), 120287.

Kim, J., Buffenstein, R., Bronikowski, A. M., Pilar Vanegas, N.-D., Rosas, L., Agudelo-Garcia, P., Mora, A. L., Rojas, M., Englund, D. A., LeBrasseur, N. K., Nunes, A., Robbins, P. D., Kohut, M. L., Kothadiya, S., Bardhan, R., Camell, C. D., Sturmlechner, I., Goronzy, J. J., Yeh, C.-Y., Lamming, D. W., Huang, S., Leiser, S. F., Escorcia, W., Gill, M., S., Taylor, J. R., Helfand, S. L., Korm, S.Gribble, K. E., Pehar, M., Blaszkiewicz, M., Townsend, K. L., McGregor, E. R., Anderson, R. M., Stilgenbauer, L., Sadagurski, M., Taylor, A., McNeill, E., Stoeger, T., & Bai, H. (2024). The Fourth Annual Symposium of the Midwest Aging Consortium. The Journals of Gerontology: Series A79(11), glae236.

Ni, Z.Neifert, C.Rosete, A., Albeely, A. M.Yang, Y.Pratelli, M.Brecht, M., & Clemens, A. M. (2024). Tactile mechanisms and afferents underlying the rat pup transport response. Current Biology.

Seaver, G. A., & Kuzirian, A. M. (2024). Estuary Nitrate Sources and Trends in Buzzards Bay. Journal of Coastal Research40(6), 1055–1067.

Kwiatkowski, E. R., Rosenthal, J. J. C., & Emery, P. (2024). Crosstalk between the circatidal and circadian clocks mediates behavioral adaptation to tidal patterns. Current Biology.

Oikawa, P. Y., Sihi, D., Forbrich, I., Fluet-Chouinard, E., Najarro, M., Thomas, O., Shahan, J., Arias-Ortiz, A., Russell, S., Knox, S. H., Mcnicol, G., Wolfe, J., Windham-Myers, L., Stuart-Haentjens, E., Bridgham, S. D., Needelman, B., Vargas, R., Schafer, K., Ward, E. J., Megonigal, P., & Holmquist, J. (2024). A New Coupled Biogeochemical Modeling Approach Provides Accurate Predictions of Methane and Carbon Dioxide Fluxes Across Diverse Tidal Wetlands. Journal of Geophysical Research: Biogeosciences129(10), e2023JG007943.

Attah, A. T.Negrón-Moreno, P. N., Amigo-Duran, M.Zhang, L.Kenngott, M.Brecht, M., & Clemens, A. M. (2024). Sensory cues, behavior and fur-based drying in the rat wetness response. Scientific Reports14, 24550. 

Gemmell, B. J., Colin, S. P., & Costello, J. H. (2024). Hydromechanical properties of metachronal swimming in polychaetes. Scientific Reports14, 24374.