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CES-Funded Publications

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

Michelle L. JohnsonBruce A. Hay & Maciej Maselko 

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

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

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

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. ShihBiomolecules 2023, 13(4), 596; Mar 26, 2023

https://doi.org/10.3390/biom13040596

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

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. bioRxiv, 566113; Dec 11, 2023

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

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

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

Tracing energy inputs into the seafloor using carbonate sediments

Smith BP, Edie SM, Fischer WW. PNASFeb 21, 2023

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

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

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

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

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

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

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/

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. TrowerJustin V. StraussErik A. SperlingWoodward W. Fischer, Geobiology, Volume 19, Issue 5, September 2021

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

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

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

CES-Funded Preprints

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

The proteome is a terminal electron acceptor

Avi I. Flamholz, Akshit Goyal, Woodward W. Fischer, Dianne K. Newman, Rob Phillips, bioRxiv [Preprint]. Feb 1, 2024

https://doi.org/10.1101/2024.01.31.578293

Annotation-free prediction of microbial dioxygen utilization

Avi I. Flamholz, Joshua E. Goldford, Elin M. Larsson, Adrian Jinich, Woodward W. Fischer, Dianne K. Newman, bioRxiv [Preprint]. Jan 16, 2024

https://doi.org/10.1101/2024.01.16.575888

​​

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/

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

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/

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

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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