Seth Shipman, PhD

Title(s)Associate Professor, Bioengineering
SchoolSchool of Pharmacy
Address1700 4th Street, #501
San Francisco CA 94158
Phone415-734-4058
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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
    Defense Advanced Research Projects Agency (DARPA)2018DARPA Riser, DARPA 60th Anniversary Symposium
    Simonds Foundation Autism Research Initiative (SFARI)2019Bridge to Independence Award
    ScienceNews2019The SN 10: Scientists to Watch
    National Institutes of Health2020NIH Director's New Innovator Award
    The Pew Charitable Trusts2020Pew Biomedical Scholar
    Bioengineering Institute of California2021Shu Chien Early Career Award Nominee

    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.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    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. An experimental census of retrons for DNA production and genome editing. Nat Biotechnol. 2024 Sep 17. Khan AG, Rojas-Montero M, González-Delgado A, Lopez SC, Fang RF, Crawford KD, Shipman SL. PMID: 39289529.
      View in: PubMed   Mentions: 1     Fields:    
    2. Continuous multiplexed phage genome editing using recombitrons. Nat Biotechnol. 2024 Sep 05. Fishman CB, Crawford KD, Bhattarai-Kline S, Poola D, Zhang K, González-Delgado A, Rojas-Montero M, Shipman SL. PMID: 39237706.
      View in: PubMed   Mentions: 6     Fields:    
    3. Simultaneous multi-site editing of individual genomes using retron arrays. Nat Chem Biol. 2024 Nov; 20(11):1482-1492. González-Delgado A, Lopez SC, Rojas-Montero M, Fishman CB, Shipman SL. PMID: 38982310; PMCID: PMC11512673.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    4. High Throughput Variant Libraries and Machine Learning Yield Design Rules for Retron Gene Editors. bioRxiv. 2024 Jul 09. Crawford KD, Khan AG, Lopez SC, Goodarzi H, Shipman SL. PMID: 39026735; PMCID: PMC11257497.
      View in: PubMed   Mentions:
    5. Limitations of fluorescent timer protein maturation kinetics to isolate transcriptionally synchronized human neural progenitor cells. iScience. 2024 Jun 21; 27(6):109911. Peter M, Shipman S, Heo J, Macklis JD. PMID: 38784012; PMCID: PMC11111830.
      View in: PubMed   Mentions:
    6. Directed differentiation of functional corticospinal-like neurons from endogenous SOX6+/NG2+ cortical progenitors. bioRxiv. 2024 Apr 23. Ozkan A, Padmanabhan HK, Shipman SL, Azim E, Kumar P, Sadegh C, Basak AN, Macklis JD. PMID: 38712174; PMCID: PMC11071355.
      View in: PubMed   Mentions:
    7. An experimental census of retrons for DNA production and genome editing. bioRxiv. 2024 Jan 26. Khan AG, Rojas-Montero M, González-Delgado A, Lopez SC, Fang RF, Shipman SL. PMID: 38328236; PMCID: PMC10849725.
      View in: PubMed   Mentions:
    8. Limitations of fluorescent timer protein maturation kinetics to isolate transcriptionally synchronized cortically differentiating human pluripotent stem cells. bioRxiv. 2023 Aug 26. Peter M, Shipman S, Macklis JD. PMID: 37609140; PMCID: PMC10441295.
      View in: PubMed   Mentions:
    9. A High-Throughput Colocalization Pipeline for Quantification of Mitochondrial Targeting across Different Protein Types. ACS Synth Biol. 2023 08 18; 12(8):2498-2504. Lear SK, Nunez JA, Shipman SL. PMID: 37506292; PMCID: PMC10561668.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    10. Simultaneous multi-site editing of individual genomes using retron arrays. bioRxiv. 2023 Jul 17. González-Delgado A, Lopez SC, Rojas-Montero M, Fishman CB, Shipman SL. PMID: 37503029; PMCID: PMC10370050.
      View in: PubMed   Mentions:
    11. Temporally resolved transcriptional recording in E. coli DNA using a Retro-Cascorder. Nat Protoc. 2023 Jun; 18(6):1866-1892. Lear SK, Lopez SC, González-Delgado A, Bhattarai-Kline S, Shipman SL. PMID: 37059915; PMCID: PMC10631475.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    12. High-throughput colocalization pipeline quantifies efficacy of mitochondrial targeting signals across different protein types. bioRxiv. 2023 Apr 03. Lear SK, Nunez JA, Shipman SL. PMID: 37066162; PMCID: PMC10103990.
      View in: PubMed   Mentions:
    13. Continuous Multiplexed Phage Genome Editing Using Recombitrons. bioRxiv. 2023 Mar 25. Fishman CB, Crawford KD, Bhattarai-Kline S, Zhang K, González-Delgado A, Shipman SL. PMID: 36993281; PMCID: PMC10055335.
      View in: PubMed   Mentions:
    14. Molecular recording: transcriptional data collection into the genome. Curr Opin Biotechnol. 2023 02; 79:102855. Lear SK, Shipman SL. PMID: 36481341; PMCID: PMC10547096.
      View in: PubMed   Mentions: 6     Fields:    
    15. Recording gene expression order in DNA by CRISPR addition of retron barcodes. Nature. 2022 08; 608(7921):217-225. Bhattarai-Kline S, Lear SK, Fishman CB, Lopez SC, Lockshin ER, Schubert MG, Nivala J, Church GM, Shipman SL. PMID: 35896746; PMCID: PMC9357182.
      View in: PubMed   Mentions: 25     Fields:    Translation:Cells
    16. Retron reverse transcriptase termination and phage defense are dependent on host RNase H1. Nucleic Acids Res. 2022 04 08; 50(6):3490-3504. Palka C, Fishman CB, Bhattarai-Kline S, Myers SA, Shipman SL. PMID: 35293583; PMCID: PMC8989520.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    17. Precise genome editing across kingdoms of life using retron-derived DNA. Nat Chem Biol. 2022 02; 18(2):199-206. Lopez SC, Crawford KD, Lear SK, Bhattarai-Kline S, Shipman SL. PMID: 34949838; PMCID: PMC8810715.
      View in: PubMed   Mentions: 34     Fields:    Translation:HumansAnimalsCells
    18. 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). Schubert MG, Goodman DB, Wannier TM, Kaur D, Farzadfard F, Lu TK, Shipman SL, Church GM. PMID: 33906944; PMCID: PMC8106316.
      View in: PubMed   Mentions: 41     Fields:    Translation:AnimalsCells
    19. 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: 4     Fields:    
    20. 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; PMCID: PMC7990699.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    21. 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; PMCID: PMC7610615.
      View in: PubMed   Mentions: 78     Fields:    Translation:HumansCells
    22. 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; PMCID: PMC5832444.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    23. 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; PMCID: PMC5842791.
      View in: PubMed   Mentions: 85     Fields:    Translation:Cells
    24. Molecular recordings by directed CRISPR spacer acquisition. Science. 2016 Jul 29; 353(6298):aaf1175. Shipman SL, Nivala J, Macklis JD, Church GM. PMID: 27284167; PMCID: PMC4994893.
      View in: PubMed   Mentions: 82     Fields:    Translation:Cells
    25. 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; PMCID: PMC9381026.
      View in: PubMed   Mentions: 80     Fields:    Translation:HumansAnimalsCells
    26. 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; PMCID: PMC4299601.
      View in: PubMed   Mentions: 127     Fields:    Translation:HumansCells
    27. 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; PMCID: PMC3943352.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansAnimalsCells
    28. 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; PMCID: PMC3742921.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    29. 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; PMCID: PMC3511127.
      View in: PubMed   Mentions: 34     Fields:    Translation:AnimalsCells
    30. 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; PMCID: PMC3998838.
      View in: PubMed   Mentions: 58     Fields:    Translation:HumansAnimalsCells
    31. 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; PMCID: PMC3171182.
      View in: PubMed   Mentions: 65     Fields:    Translation:AnimalsCells
    32. 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; PMCID: PMC2702996.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    33. 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: 30     Fields:    Translation:Humans
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