Seth Shipman, PhD

Associate Professor
Department of Bioengineering and Therapeutic Sciences
Shipman
[email protected]
Phone: +1 415 734-4058
1700 4th Street, Rm 501
UCSF Box 1230
San Francisco, CA 94158
United States

Links

Shipman Lab UCSF Profiles Gladstone Institutes

Affiliations

Joint appointments

Associate Investigator, Gladstone Institute of Data Science and Biotechnology

What I do

My lab develops molecular biotechnology to overcome technical hurdles that prevent us from effectively understanding and treating disease. We're particularly interested in neurodevelopmental and neurodegenerative disease.

Departmental research area

pharmacogenomics and genomics
therapeutic bioengineering

Professional background

Degrees

PhD, University of California, San Francisco, 2012

Biography

Dr. Seth Shipman's research focuses on cellular systems in the midst of change. His lab seeks to better understand how the order of transcriptional events during development can drive changes in cell fate, and to better intervene in diseases characterized by change, like progressive neurodegeneration and cancer. His lab takes a molecular engineering approach, leveraging the versatility of DNA as a programmable biological polymer to gather data without destroying cells, and deliver therapeutics that can modify their effect based on cell context.

Research keywords

  • RNA-Directed DNA Polymerase
  • Genome, Bacterial
  • CRISPR-Cas Systems
  • Escherichia coli Proteins
  • Information Storage and Retrieval
  • Gene Expression Regulation, Bacterial
  • DNA
  • Cell Adhesion Molecules, Neuronal
  • Protein Sorting Signals
  • Motion Pictures
  • E. coli
  • Reverse Transcription
  • Gene Editing
  • Bacteriophages
  • Clustered Regularly Interspaced Short Palindromic Repeats
1. Update from the Dean: Ongoing excellence and new frontiers
2. Shipman lab develops a biological recorder of gene expression
3. Update from the Dean: Passing the torch
4. Faculty members inducted into the Chan Zuckerberg Biohub Investigator Program
5. Shipman lab pioneers more efficient genome editing
6. Update from the Dean: Community during challenging times
7. Shipman receives NIH Director’s New Innovator Award
1. Shu Chien Early Career Award Nominee, Bioengineering Institute of California, 2021
2. NIH Director's New Innovator Award, National Institutes of Health, 2020
3. Pew Biomedical Scholar, The Pew Charitable Trusts, 2020
4. The SN 10: Scientists to Watch, ScienceNews, 2019
5. Bridge to Independence Award, Simonds Foundation Autism Research Initiative (SFARI), 2019
6. DARPA Riser, DARPA 60th Anniversary Symposium, Defense Advanced Research Projects Agency (DARPA), 2018
7. Postdoctoral Award, Life Science Research Foundation, 2014
8. Travel Award, Earle C. Anthony, 2012
9. Poster Award, Gordon Research Conference, 2012
10. Grass Fellowship in Neuroscience (declined), Grass Foundation, 2011
11. Graduate Research Fellowship, Honorable Mention, National Science Foundation, 2007-2008
12. Outstanding Physics Student Scholarship, Wesleyan University, 2001

Publications

Wang L, Poulis N, Srivastava D, Shipman SL. MitoScribe single-cell molecular recorder logs graded signaling dynamics into mitochondrial DNA. bioRxiv. 2025 Sep 05.
González-Delgado A, Bonillo-Lopez L, Johnson MS, Knödlseder N, Ko CC, Lekbach Y, Oh JH, Selvakumar H, Wold MC, Yu Z, Aragón V, Gralnick JA, Güell M, Hatfull GF, Keitz BK, Koskella B, Mutalik VK, van Pijkeren JP, Shipman SL. Genome editing of phylogenetically distinct bacteria using portable retron-mediated recombineering. bioRxiv. 2025 Jul 09.
Lopez SC, Lee Y, Zhang K, Shipman SL. SspA is a transcriptional regulator of CRISPR adaptation in E. coli. Nucleic Acids Res. 2025 Feb 08; 53(4).
Crawford KD, Khan AG, Lopez SC, Goodarzi H, Shipman SL. High throughput variant libraries and machine learning yield design rules for retron gene editors. Nucleic Acids Res. 2025 Jan 11; 53(2).
Khan AG, Rojas-Montero M, González-Delgado A, Lopez SC, Fang RF, Crawford KD, Shipman SL. An experimental census of retrons for DNA production and genome editing. Nat Biotechnol. 2024 Sep 17.
Fishman CB, Crawford KD, Bhattarai-Kline S, Poola D, Zhang K, González-Delgado A, Rojas-Montero M, Shipman SL. Continuous multiplexed phage genome editing using recombitrons. Nat Biotechnol. 2024 Sep 05.
Crawford KD, Khan AG, Lopez SC, Goodarzi H, Shipman SL. High Throughput Variant Libraries and Machine Learning Yield Design Rules for Retron Gene Editors. bioRxiv. 2024 Jul 09.
González-Delgado A, Lopez SC, Rojas-Montero M, Fishman CB, Shipman SL. Simultaneous multi-site editing of individual genomes using retron arrays. Nat Chem Biol. 2024 Nov; 20(11):1482-1492.
Peter M, Shipman S, Heo J, Macklis JD. Limitations of fluorescent timer protein maturation kinetics to isolate transcriptionally synchronized human neural progenitor cells. iScience. 2024 Jun 21; 27(6):109911.
Ozkan A, Padmanabhan HK, Shipman SL, Azim E, Kumar P, Sadegh C, Basak AN, Macklis JD. Directed differentiation of functional corticospinal-like neurons from endogenous SOX6+/NG2+ cortical progenitors. bioRxiv. 2024 Apr 23.
Khan AG, Rojas-Montero M, González-Delgado A, Lopez SC, Fang RF, Shipman SL. An experimental census of retrons for DNA production and genome editing. bioRxiv. 2024 Jan 26.
Peter M, Shipman S, Macklis JD. Limitations of fluorescent timer protein maturation kinetics to isolate transcriptionally synchronized cortically differentiating human pluripotent stem cells. bioRxiv. 2023 Aug 26.
Lear SK, Nunez JA, Shipman SL. A High-Throughput Colocalization Pipeline for Quantification of Mitochondrial Targeting across Different Protein Types. ACS Synth Biol. 2023 08 18; 12(8):2498-2504.
González-Delgado A, Lopez SC, Rojas-Montero M, Fishman CB, Shipman SL. Simultaneous multi-site editing of individual genomes using retron arrays. bioRxiv. 2023 Jul 17.
Lear SK, Lopez SC, González-Delgado A, Bhattarai-Kline S, Shipman SL. Temporally resolved transcriptional recording in E. coli DNA using a Retro-Cascorder. Nat Protoc. 2023 06; 18(6):1866-1892.
Lear SK, Nunez JA, Shipman SL. High-throughput colocalization pipeline quantifies efficacy of mitochondrial targeting signals across different protein types. bioRxiv. 2023 Apr 03.
Fishman CB, Crawford KD, Bhattarai-Kline S, Zhang K, González-Delgado A, Shipman SL. Continuous Multiplexed Phage Genome Editing Using Recombitrons. bioRxiv. 2023 Mar 25.
Lear SK, Shipman SL. Molecular recording: transcriptional data collection into the genome. Curr Opin Biotechnol. 2023 02; 79:102855.
Bhattarai-Kline S, Lear SK, Fishman CB, Lopez SC, Lockshin ER, Schubert MG, Nivala J, Church GM, Shipman SL. Recording gene expression order in DNA by CRISPR addition of retron barcodes. Nature. 2022 08; 608(7921):217-225.
Palka C, Fishman CB, Bhattarai-Kline S, Myers SA, Shipman SL. Retron reverse transcriptase termination and phage defense are dependent on host RNase H1. Nucleic Acids Res. 2022 04 08; 50(6):3490-3504.
Lopez SC, Crawford KD, Lear SK, Bhattarai-Kline S, Shipman SL. Precise genome editing across kingdoms of life using retron-derived DNA. Nat Chem Biol. 2022 02; 18(2):199-206.
Schubert MG, Goodman DB, Wannier TM, Kaur D, Farzadfard F, Lu TK, Shipman SL, Church GM. High-throughput functional variant screens via in vivo production of single-stranded DNA. Proc Natl Acad Sci U S A. 2021 05 04; 118(18).
Bhattarai-Kline S, Lear SK, Shipman SL. One-step data storage in cellular DNA. Nat Chem Biol. 2021 03; 17(3):232-233.
Filsinger GT, Wannier TM, Pedersen FB, Lutz ID, Zhang J, Stork DA, Debnath A, Gozzi K, Kuchwara H, Volf V, Wang S, Rios X, Gregg CJ, Lajoie MJ, Shipman SL, Aach J, Laub MT, Church GM. Characterizing the portability of phage-encoded homologous recombination proteins. Nat Chem Biol. 2021 04; 17(4):394-402.
Ng AHM, Khoshakhlagh P, Rojo Arias JE, Pasquini G, Wang K, Swiersy A, Shipman SL, Appleton E, Kiaee K, Kohman RE, Vernet A, Dysart M, Leeper K, Saylor W, Huang JY, Graveline A, Taipale J, Hill DE, Vidal M, Melero-Martin JM, Busskamp V, Church GM. A comprehensive library of human transcription factors for cell fate engineering. Nat Biotechnol. 2021 04; 39(4):510-519.
Nivala J, Shipman SL, Church GM. Spontaneous CRISPR loci generation in vivo by non-canonical spacer integration. Nat Microbiol. 2018 03; 3(3):310-318.
Shipman SL, Nivala J, Macklis JD, Church GM. CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria. Nature. 2017 07 20; 547(7663):345-349.
Shipman SL, Nivala J, Macklis JD, Church GM. Molecular recordings by directed CRISPR spacer acquisition. Science. 2016 Jul 29; 353(6298):aaf1175.
Bemben MA, Shipman SL, Nicoll RA, Roche KW. The cellular and molecular landscape of neuroligins. Trends Neurosci. 2015 Aug; 38(8):496-505.
Busskamp V, Lewis NE, Guye P, Ng AH, Shipman SL, Byrne SM, Sanjana NE, Murn J, Li Y, Li S, Stadler M, Weiss R, Church GM. Rapid neurogenesis through transcriptional activation in human stem cells. Mol Syst Biol. 2014 Nov 17; 10:760.
Bemben MA, Shipman SL, Hirai T, Herring BE, Li Y, Badger JD, Nicoll RA, Diamond JS, Roche KW. CaMKII phosphorylation of neuroligin-1 regulates excitatory synapses. Nat Neurosci. 2014 Jan; 17(1):56-64.
Shipman SL, Herring BE, Suh YH, Roche KW, Nicoll RA. Distance-dependent scaling of AMPARs is cell-autonomous and GluA2 dependent. J Neurosci. 2013 Aug 14; 33(33):13312-9.
Shipman SL, Nicoll RA. Dimerization of postsynaptic neuroligin drives synaptic assembly via transsynaptic clustering of neurexin. Proc Natl Acad Sci U S A. 2012 Nov 20; 109(47):19432-7.
Shipman SL, Nicoll RA. A subtype-specific function for the extracellular domain of neuroligin 1 in hippocampal LTP. Neuron. 2012 Oct 18; 76(2):309-16.
Shipman SL, Schnell E, Hirai T, Chen BS, Roche KW, Nicoll RA. Functional dependence of neuroligin on a new non-PDZ intracellular domain. Nat Neurosci. 2011 Jun; 14(6):718-26.
Shipman SL, Baker EK, Pearlson G, Astur RS. Absence of established sex differences in patients with schizophrenia on a two-dimensional object array task. Psychiatry Res. 2009 Apr 30; 166(2-3):158-65.
Shipman SL, Astur RS. Factors affecting the hippocampal BOLD response during spatial memory. Behav Brain Res. 2008 Mar 05; 187(2):433-41.