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CES-Funded Publications

Evolutionary basis of intermale sexual behavior by multiple pheromone switches in Drosophila

Youcef Ouadah, Thomas H. Naragon, Hayley Smihula, Emily L. Behrman, Mohammed A. Khallaf,  View Yun Ding, David L. Stern, Joseph Parker, David J. Anderson, Current Biology, vol. 36, Issue 7, April 6, 2026

https://www.cell.com/current-biology/fulltext/S0960-9822(26)00233-2

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Strain matters: host responses reflect symbiont origin in the squid-vibrio symbiosis

Vera Beilinson, Grischa Y. Chen, Alexis C. Hargadon, Edward G. Ruby, Margaret J. McFall-Ngai

Beilinson V, Chen GY, Hargadon AC, Ruby EG, McFall-Ngai MJ. mSystems vol. 10, No. 12, November 17, 2025

https://journals.asm.org/doi/full/10.1128/msystems.00498-25

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Cross-reactive sarbecovirus antibodies induced by mosaic RBD-nanoparticles

Chengcheng Fan, Jennifer R Keeffe, Kathryn E Malecek, Alexander A Cohen, Anthony P West Jr, Viren A Baharani, Annie V Rorick, Han Gao, Priyanthi N P Gnanapragasam, Semi Rho, Jaasiel Alvarez, Luisa N Segovia, Theodora Hatziioannou, Paul D Bieniasz, Pamela J Bjorkman, PNAS, vol. 122, No. 2, May 22, 2025

https://www.pnas.org/doi/10.1073/pnas.2501637122

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Recalibrating Olfactory Neuroscience to the Range of Naturally Occurring Odor Concentrations

Matt Wachowiak, Adam Dewan, Thomas Bozza, Tom F. O’Connell and Elizabeth J. Hong, Journal of Neuroscience, 45, March 5, 2025

https://www.jneurosci.org/content/45/10/e1872242024.abstract

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Evidence for Low Dissolved Silica in mid-Mesozoic Oceans

Joyce A. Yager, A. Joshua West, Elizabeth J. Trower, Woodward W. Fischer, Kathleen Ritterbush, Silvia Rosas, David J. Bottjer, Aaron J. Celestian, William M. Berelson, Frank A. Corsetti, American Journal of Science, 325, January 8, 2025

https://ajsonline.org/article/122691-evidence-for-low-dissolved-silica-in-mid-mesozoic-oceans

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The proteome is a terminal electron acceptor

Avi I. Flamholz, Akshit Goyal, Woodward W. Fischer, Dianne K. Newman, Rob Phillips, PNAS 122, 1, January 3, 2025

https://www.pnas.org/doi/abs/10.1073/pnas.2404048121​​​

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Annotation-free prediction of microbial dioxygen utilization

Avi I. Flamholz, Joshua E. Goldford, Elin M. Larsson, Adrian Jinich, Woodward W. Fischer, Dianne K. Newman, M Systems, Vol 9, No. 10, Sept 4, 2024

https://journals.asm.org/doi/full/10.1128/msystems.00763-24

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Altering traits and fates of wild populations with Mendelian DNA sequence modifying Allele Sails

Michelle L. Johnson, Bruce A. Hay & Maciej Maselko 

Nature Communications volume 15, Article number: 6665 (2024), Aug 13, 2024

https://www.nature.com/articles/s41467-024-50992-9

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The Genomic and Cellular Basis of Biosynthetic Innovation in Rove Beetles

Kitchen, S.A. , Naragon, T. H.,Brückner, A, Ladinsky, M. S., Quinodoz, S. A., Badroos, J.M., Viliunas, J.W., Kishi, Y., Wagner, J.M., Miller, D.R., Yousefelahiyeh, M., Antoshechkin, I.A., Eldredge, K.T., Pirro, S., Guttman, M., Davis, S.R., Aardema, M.L., Parker, J. Cell, Jun 17, 2024

https://doi.org/10.1016/j.cell.2024.05.012

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A Bacterial Form I’ Rubisco Has a Smaller Carbon Isotope Fractionation than Its Form I Counterpart

Renée Z. Wang, Albert K. Liu, Douglas M. Banda, Woodward W. Fischer, Patrick M. Shih, Biomolecules 2023, 13(4), 596; Mar 26, 2023

https://doi.org/10.3390/biom13040596

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Syntactic Structures and the General Markov Models

Gakkhar, S., Marcolli, M.  Math.Comput.Sci. 18, Mar 7, 2024

https://doi.org/10.1007/s11786-023-00575-6​

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Molecular identification of a peroxidase gene controlling body size in the entomopathogenic nematode Steinernema hermaphroditum

Schwartz HT, Tan CH, Peraza J, Raymundo KLT, Sternberg, P. Genetics, Volume 226, Issue 2, February 2024

https://academic.oup.com/genetics/article/226/2/iyad209/7469079

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Exploring uranium isotopes in shark teeth as a paleo-redox proxy

Li H, Kipp MA, Kim SL, Kast ER, Eberle JJ, Tissot FL, Geochimica et Cosmochimica Acta. Dec 2, 2023

https://doi.org/10.1016/j.gca.2023.11.034

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Manipulating the destiny of wild populations using CRISPR

Raban R, Marshall JM, Hay BA, Akbari OS, Annual Review of Genetics; 57. Sept 18, 2023

https://www.annualreviews.org/doi/abs/10.1146/annurev-genet-031623-105059​

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Tracing energy inputs into the seafloor using carbonate sediments

Smith BP, Edie SM, Fischer WW. PNAS, Feb 21, 2023

https://doi.org/10.1073/pnas.2215833120

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Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes

Wu F, Speth DR, Philosof A, Crémière A, Narayanan A, Barco RA, Connon SA, Amend JP, Antoshechkin IA, Orphan VJ., Nature Microbiology, 7(2):200-12, Feb 2022

https://www.nature.com/articles/s41564-021-01039-y

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The Wonders of Jellyfish Dajose, L.,  Caltech Magazine 85, no. 1 (2022)

https://magazine.caltech.edu/post/the-wonders-of-jellyfish

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The entomopathogenic nematode Steinernema hermaphroditum is a self-fertilizing hermaphrodite and a genetically tractable system for the study of parasitic and mutualistic symbiosis

Cao M, Schwartz HT, Tan CH, Sternberg PW, Genetics. 220(1):iyab170. doi: 10.1093/genetics/iyab170. PMID: 34791196; PMCID: PMC8733455. Jan 4, 2022

https://doi.org/10.1093/genetics/iyad209

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A conserved strategy for inducing appendage regeneration in moon jellyfish, Drosophila, and mice

Abrams MJ, Tan FH, Li Y, Basinger T, Heithe ML, Sarma A, Lee IT, Condiotte ZJ, Raffiee M, Dabiri JO, Gold DA, Goentoro L., Elife;10:e65092. doi: 10.7554/eLife.65092. Erratum in: Elife. 22;12: PMID: 34874003; PMCID: PMC8782573, Dec 7, 2021

https://doi.org/10.7554/eLife.65092

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Whole-animal multiplexed single-cell RNA-seq reveals transcriptional shifts across Clytia medusa cell types 

Chari T, Weissbourd B, Gehring J, Ferraioli A, Leclère L, Herl M, Gao F, Chevalier S, Copley RR, Houliston E, Anderson DJ. Science Advances. 7(48):eabh1683. Nov 26, 2021

https://www.science.org/doi/full/10.1126/sciadv.abh1683

 

A genetically tractable jellyfish model for systems and evolutionary neuroscience Weissbourd B, Momose T, Nair A, Kennedy A, Hunt B, Anderson DJ., Cell. 184(24):5854-5868.e20. doi: 10.1016/j.cell.2021.10.021. PMID: 34822783; PMCID: PMC8629132, Nov 24, 2021

https://pubmed.ncbi.nlm.nih.gov/34822783/

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Generator based approach to analyze mutations in genomic datasets

Jain S, Xiao X, Bogdan P, Bruck J.  Scientific Reports., 11(1):21084. Oct 26, 2021

https://www.nature.com/articles/s41598-021-00609-8

 

Isotopic analyses of Ordovician–Silurian siliceous skeletons indicate silica-depleted Paleozoic oceans

​Elizabeth J. Trower, Justin V. Strauss, Erik A. Sperling, Woodward W. Fischer, Geobiology, Volume 19, Issue 5, September 2021

https://doi.org/10.1111/gbi.12449

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A Redox‐Based Model for Carbonate Platform Drowning and Ocean Anoxic Events

Smith BP, Kerans C, Fischer WW., Geophysical Research Letters, 48(13):e2021GL093048, Jul 16, 2021

https://doi.org/10.1029/2021GL093048

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Physical controls on carbonate intraclasts: Modern flat pebbles from Great Salt Lake, Utah

Smith BP, Ingalls M, Trower EJ, Lingappa UF, Present TM, Magyar JS, Fischer WW., Journal of Geophysical Research: Earth Surface, 125(11):e2020JF005733, Nov 2020

https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2020JF005733

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CES-Funded Preprints

Threonine nitrogen isotopes reveal hidden physiological dimensions of mammalian ecology

Julia Tejada, bioRxiv [Preprint], August 19, 2026

https://www.biorxiv.org/content/10.64898/2026.08.14.744972v1.abstract

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Structural evolution of the MTCH family of mitochondrial insertases​

Taylor A. Stevens, Zhilin Luo, Camryn Lee, Masami Hazu, Erini G. Galatis, Alison J. Inglis, Alina Guna, Rebecca M. Voorhees, bioRxiv [Preprint], April 15, 2026

https://www.biorxiv.org/content/10.64898/2026.02.17.705849v2

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​Evolution of parasitism-related traits in nematodes

Chieh-Hsiang Tan, Hillel T. Schwartz,  Nathan Y. Rodak, Paul W Sternberg, bioRxiv [Preprint], September 27, 2025

https://www.biorxiv.org/content/10.1101/2025.09.26.678730

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Allele Sails: launching traits and fates into wild populations with Mendelian DNA sequence modifiers

Michelle L. Johnson, Bruce A. Hay, Maciej Maselko, bioRxiv [Preprint], April 10, 2024

https://doi.org/10.1101/2024.03.18.585647

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Recovery of a learned behavior despite partial restoration of neuronal dynamics after chronic inactivation of inhibitory neurons 

Torok Z, Luebbert L, Feldman J, Duffy A, Nevue AA, Wongso S, Mello CV, Fairhall A, Pachter L, Gonzalez WG, Lois C., bioRxiv [Preprint]. doi: 10.1101/2023.05.17.541057. PMID: 37292888; PMCID: PMC10245685, Dec 15, 2023

https://pubmed.ncbi.nlm.nih.gov/37292888/

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Syntax-semantics interface: an algebraic model

Marcolli M, Berwick RC, Chomsky N., arXiv preprint arXiv:2311.06189., Nov 10, 2023

https://doi.org/10.48550/arXiv.2311.06189

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Cleave and Rescue gamete killers create conditions for gene drive in plants

Oberhofer G, Johnson ML, Ivy T, Hay BA., bioRxiv. Oct 14, 2023

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10592828/

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Old and New Minimalism: a Hopf algebra comparison

Marcolli M, Berwick RC, Chomsky N., arXiv preprint arXiv:2306.10270. Jun 17, 2023

https://doi.org/10.48550/arXiv.2306.10270

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Mathematical Structure of Syntactic Merge

Marcolli M, Chomsky N, Berwick R., arXiv preprint arXiv:2305.18278. May 29, 2023

https://doi.org/10.48550/arXiv.2305.18278

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