Seth Shipman, PhD

Title(s)Assistant Professor, Bioengineering
SchoolSchool of Pharmacy
Address1650 Owens Street
San Francisco CA 94158
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    Collapse Biography 
    Collapse Education and Training
    Wesleyan University, ConnecticutB.A.05/2005Neuroscience
    University of California, San Francisco, San FranciscoPh.D.12/2012Neuroscience
    Harvard Medicall School, BostonPostdoctoral Fellowship10/2018Genetics, Synthetic Biology, Stem Cell Biology
    Collapse Awards and Honors
    Wesleyan University2001Outstanding Physics Student Scholarship
    National Science Foundation2007  - 2008Graduate Research Fellowship, Honorable Mention
    Grass Foundation2011Grass Fellowship in Neuroscience (declined)
    Earle C. Anthony2012Travel Award
    Gordon Research Conference2012Poster Award
    Life Science Research Foundation2014Postdoctoral Award
    DARPA2018DARPA Riser, DARPA 60th Anniversity Symposium
    Simonds Foundation Autism Research Initiative (SFARI)2019Bridge to Indipendence Award
    ScienceNews2019The SN 10: Scientists to Watch

    Collapse Overview 
    Collapse Overview
    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.

    Collapse Research 
    Collapse Research Activities and Funding
    Engineered Mitochondria for Therapeutic Donation and Mitochondrial Genome Editing
    NIH DP2GM140917Sep 30, 2020 - May 31, 2025
    Role: Principal Investigator
    Reconstructing the Cellular History of Neurons Using Molecular Recordings
    Simons Foundation Autism Resarch Initiative (SFARI) Bridge to IndependenceJan 1, 2019 - Jan 1, 2022
    Role: PI
    Human Gene Editing and In Situ Sequencing of Neuronal Microcircuit Arrays
    Simons Foundation Autism Research Initiative (SFARI) Pilot AwardAug 1, 2015 - Jan 1, 2017
    Role: Postdoctoral Fellow
    New molecular tools to investigate transcriptional networds that govern cell-fate decisions at the single-cell level during neuronal differentiation
    Life Sciences Research Foundation Shurl and Kay Curci Foundation FellowshipNov 15, 2014 - Nov 14, 2017
    Role: PI
    Recording neural activities onto DNA
    NIH R01MH103910Sep 26, 2013 - Aug 31, 2018
    Role: Postdoctoral Fellow

    Collapse ORNG Applications 
    Collapse Featured Publications

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. High-throughput functional variant screens via in vivo production of single-stranded DNA. Proc Natl Acad Sci U S A. 2021 May 04; 118(18). Schubert MG, Goodman DB, Wannier TM, Kaur D, Farzadfard F, Lu TK, Shipman SL, Church GM. PMID: 33906944.
      View in: PubMed   Mentions:    Fields:    
    2. One-step data storage in cellular DNA. Nat Chem Biol. 2021 03; 17(3):232-233. Bhattarai-Kline S, Lear SK, Shipman SL. PMID: 33500580.
      View in: PubMed   Mentions:    Fields:    
    3. Characterizing the portability of phage-encoded homologous recombination proteins. Nat Chem Biol. 2021 04; 17(4):394-402. 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. PMID: 33462496.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    4. A comprehensive library of human transcription factors for cell fate engineering. Nat Biotechnol. 2021 04; 39(4):510-519. 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. PMID: 33257861.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    5. Spontaneous CRISPR loci generation in vivo by non-canonical spacer integration. Nat Microbiol. 2018 03; 3(3):310-318. Nivala J, Shipman SL, Church GM. PMID: 29379209.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    6. 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. PMID: 28700573.
      View in: PubMed   Mentions: 37     Fields:    Translation:Cells
    7. Molecular recordings by directed CRISPR spacer acquisition. Science. 2016 Jul 29; 353(6298):aaf1175. Shipman SL, Nivala J, Macklis JD, Church GM. PMID: 27284167.
      View in: PubMed   Mentions: 37     Fields:    Translation:Cells
    8. The cellular and molecular landscape of neuroligins. Trends Neurosci. 2015 Aug; 38(8):496-505. Bemben MA, Shipman SL, Nicoll RA, Roche KW. PMID: 26209464.
      View in: PubMed   Mentions: 47     Fields:    Translation:HumansAnimalsCells
    9. Rapid neurogenesis through transcriptional activation in human stem cells. Mol Syst Biol. 2014 Nov 17; 10:760. 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. PMID: 25403753.
      View in: PubMed   Mentions: 68     Fields:    Translation:HumansCells
    10. CaMKII phosphorylation of neuroligin-1 regulates excitatory synapses. Nat Neurosci. 2014 Jan; 17(1):56-64. Bemben MA, Shipman SL, Hirai T, Herring BE, Li Y, Badger JD, Nicoll RA, Diamond JS, Roche KW. PMID: 24336150.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansAnimalsCells
    11. Distance-dependent scaling of AMPARs is cell-autonomous and GluA2 dependent. J Neurosci. 2013 Aug 14; 33(33):13312-9. Shipman SL, Herring BE, Suh YH, Roche KW, Nicoll RA. PMID: 23946389.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    12. 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. PMID: 23129658.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
    13. A subtype-specific function for the extracellular domain of neuroligin 1 in hippocampal LTP. Neuron. 2012 Oct 18; 76(2):309-16. Shipman SL, Nicoll RA. PMID: 23083734.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansAnimalsCells
    14. Functional dependence of neuroligin on a new non-PDZ intracellular domain. Nat Neurosci. 2011 Jun; 14(6):718-26. Shipman SL, Schnell E, Hirai T, Chen BS, Roche KW, Nicoll RA. PMID: 21532576.
      View in: PubMed   Mentions: 53     Fields:    Translation:AnimalsCells
    15. 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, Baker EK, Pearlson G, Astur RS. PMID: 19278735.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    16. Factors affecting the hippocampal BOLD response during spatial memory. Behav Brain Res. 2008 Mar 05; 187(2):433-41. Shipman SL, Astur RS. PMID: 18055028.
      View in: PubMed   Mentions: 27     Fields:    Translation:Humans
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