Publications by authors named "Seth Shipman"

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New retron systems from environmental bacteria identify triggers of anti-phage defense and expand tools for genome editing.
Kazuo L Nakamura, Karen Zhang, Mario R Mestre, Matías Rojas-Montero, Seth L Shipman

PLoS Biol· October 2025

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MitoScribe single-cell molecular recorder logs graded signaling dynamics into mitochondrial DNA.
Linhan Wang, Nikolaos Poulis, Deepak Srivastava, Seth L Shipman

bioRxiv· September 2025

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Continuous multiplexed phage genome editing using recombitrons.
Chloe B Fishman, Kate D Crawford, Santi Bhattarai-Kline, Darshini Poola, Karen Zhang, Seth L Shipman

Nat Biotechnol· August 2025

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Genome editing of phylogenetically distinct bacteria using portable retron-mediated recombineering.
Alejandro González-Delgado, Laura Bonillo-Lopez, Milo S Johnson, Nastassia Knödlseder, Ching-Chung Ko, Seth L Shipman

bioRxiv· July 2025

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An experimental census of retrons for DNA production and genome editing.
Asim G Khan, Matías Rojas-Montero, Alejandro González-Delgado, Santiago C Lopez, Rebecca F Fang, Seth L Shipman

Nat Biotechnol· June 2025

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Directed differentiation of functional corticospinal-like neurons from endogenous SOX6+/NG2+ cortical progenitors.
Abdulkadir Ozkan, Hari K Padmanabhan, Seth L Shipman, Eiman Azim, Priyanka Kumar

bioRxiv· April 2025

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SspA is a transcriptional regulator of CRISPR adaptation in E. coli.
Santiago C Lopez, Yumie Lee, Karen Zhang, Seth L Shipman

Nucleic Acids Res· February 2025

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High throughput variant libraries and machine learning yield design rules for retron gene editors.
Kate D Crawford, Asim G Khan, Santiago C Lopez, Hani Goodarzi, Seth L Shipman

Nucleic Acids Res· January 2025

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Simultaneous multi-site editing of individual genomes using retron arrays.
Alejandro González-Delgado, Santiago C Lopez, Matías Rojas-Montero, Chloe B Fishman, Seth L Shipman

Nat Chem Biol· November 2024

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High Throughput Variant Libraries and Machine Learning Yield Design Rules for Retron Gene Editors.
Kate D Crawford, Asim G Khan, Santiago C Lopez, Hani Goodarzi, Seth L Shipman

bioRxiv· July 2024

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Limitations of fluorescent timer protein maturation kinetics to isolate transcriptionally synchronized human neural progenitor cells.
Manuel Peter, Seth Shipman, Jaewon Heo, Jeffrey D Macklis

iScience· June 2024

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An experimental census of retrons for DNA production and genome editing.
Asim G Khan, Matías Rojas-Montero, Alejandro González-Delgado, Santiago C Lopez, Rebecca F Fang, Seth L Shipman

bioRxiv· January 2024

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A High-Throughput Colocalization Pipeline for Quantification of Mitochondrial Targeting across Different Protein Types.
Sierra K Lear, Jose A Nunez, Seth L Shipman

ACS Synth Biol· August 2023

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Limitations of fluorescent timer protein maturation kinetics to isolate transcriptionally synchronized cortically differentiating human pluripotent stem cells.
Manuel Peter, Seth Shipman, Jeffrey D Macklis

bioRxiv· August 2023

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Simultaneous multi-site editing of individual genomes using retron arrays.
Alejandro González-Delgado, Santiago C Lopez, Matías Rojas-Montero, Chloe B Fishman, Seth L Shipman

bioRxiv· July 2023

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Temporally resolved transcriptional recording in E. coli DNA using a Retro-Cascorder.
Sierra K Lear, Santiago C Lopez, Alejandro González-Delgado, Santi Bhattarai-Kline, Seth L Shipman

Nat Protoc· June 2023

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High-throughput colocalization pipeline quantifies efficacy of mitochondrial targeting signals across different protein types.
Sierra K Lear, Jose A Nunez, Seth L Shipman

bioRxiv· April 2023

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Continuous Multiplexed Phage Genome Editing Using Recombitrons.
Chloe B Fishman, Kate D Crawford, Santi Bhattarai-Kline, Karen Zhang, Alejandro González-Delgado, Seth L Shipman

bioRxiv· March 2023

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Molecular recording: transcriptional data collection into the genome.
Sierra K Lear, Seth L Shipman

Curr Opin Biotechnol· February 2023

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Recording gene expression order in DNA by CRISPR addition of retron barcodes.
Santi Bhattarai-Kline, Sierra K Lear, Chloe B Fishman, Santiago C Lopez, Elana R Lockshin, Seth L Shipman

Nature· August 2022

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Retron reverse transcriptase termination and phage defense are dependent on host RNase H1.
Christina Palka, Chloe B Fishman, Santi Bhattarai-Kline, Samuel A Myers, Seth L Shipman

Nucleic Acids Res· April 2022

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Precise genome editing across kingdoms of life using retron-derived DNA.
Santiago C Lopez, Kate D Crawford, Sierra K Lear, Santi Bhattarai-Kline, Seth L Shipman

Nat Chem Biol· February 2022

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High-throughput functional variant screens via in vivo production of single-stranded DNA.
Max G Schubert, Daniel B Goodman, Timothy M Wannier, Divjot Kaur, Fahim Farzadfard, Seth L Shipman

Proc Natl Acad Sci U S A· May 2021

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Characterizing the portability of phage-encoded homologous recombination proteins.
Gabriel T Filsinger, Timothy M Wannier, Felix B Pedersen, Isaac D Lutz, Julie Zhang, Seth L Shipman

Nat Chem Biol· April 2021

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One-step data storage in cellular DNA.
Santi Bhattarai-Kline, Sierra K Lear, Seth L Shipman

Nat Chem Biol· March 2021

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