Seth Shipman, PhD
Associate Professor
Bioengineering
School of Pharmacy
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.
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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.
Awards
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- Shu Chien Early Career Award Nominee, Bioengineering Institute of California, 2021
- NIH Director's New Innovator Award, National Institutes of Health, 2020
- Pew Biomedical Scholar, The Pew Charitable Trusts, 2020
- The SN 10: Scientists to Watch, ScienceNews, 2019
- Bridge to Independence Award, Simonds Foundation Autism Research Initiative (SFARI), 2019
- DARPA Riser, DARPA 60th Anniversary Symposium, Defense Advanced Research Projects Agency (DARPA), 2018
- Postdoctoral Award, Life Science Research Foundation, 2014
- Travel Award, Earle C. Anthony, 2012
- Poster Award, Gordon Research Conference, 2012
- Grass Fellowship in Neuroscience (declined), Grass Foundation, 2011
- Graduate Research Fellowship, Honorable Mention, National Science Foundation, 2007-2008
- Outstanding Physics Student Scholarship, Wesleyan University, 2001
Education & Training
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- Postdoctoral Fellowship Genetics, Synthetic Biology, Stem Cell Biology Harvard Medicall School 10/2018
- Ph.D. Neuroscience University of California, San Francisco 12/2012
- B.A. Neuroscience Wesleyan University 05/2005
Websites
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- Lab Website (gladstone.org)
- Shipman Lab (shipmanlab.org)
Grants and Projects
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- Engineered Mitochondria for Therapeutic Donation and Mitochondrial Genome Editing, NIH, 2020-2025
- Reconstructing the Cellular History of Neurons Using Molecular Recordings, Simons Foundation Autism Resarch Initiative (SFARI), 2019-2022
- Recording neural activities onto DNA, NIH, 2013-2018
- New molecular tools to investigate transcriptional networds that govern cell-fate decisions at the single-cell level during neuronal differentiation, Life Sciences Research Foundation, 2014-2017
- Human Gene Editing and In Situ Sequencing of Neuronal Microcircuit Arrays, Simons Foundation Autism Research Initiative (SFARI), 2015-2017
Publications (27)
Top publication keywords:
RNA-Directed DNA PolymeraseGenome, BacterialCRISPR-Cas SystemsInformation Storage and RetrievalDNACell Adhesion Molecules, NeuronalProtein Sorting SignalsMotion PicturesEscherichia coliReverse TranscriptionNerve Tissue ProteinsGene EditingSynthetic BiologyBacteriophagesClustered Regularly Interspaced Short Palindromic Repeats
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High-throughput functional variant screens via in vivo production of single-stranded DNA.
Proceedings of the National Academy of Sciences of the United States of America 2021 Schubert MG, Goodman DB, Wannier TM, Kaur D, Farzadfard F, Lu TK, Shipman SL, Church GM -
One-step data storage in cellular DNA.
Nature chemical biology 2021 Bhattarai-Kline S, Lear SK, Shipman SL -
A comprehensive library of human transcription factors for cell fate engineering.
Nature biotechnology 2020 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, … -
CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria.
Nature 2017 Shipman SL, Nivala J, Macklis JD, Church GM -
Molecular recordings by directed CRISPR spacer acquisition.
Science (New York, N.Y.) 2016 Shipman SL, Nivala J, Macklis JD, Church GM
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An experimental census of retrons for DNA production and genome editing.
bioRxiv : the preprint server for biology 2024 Khan AG, Rojas-Montero M, González-Delgado A, Lopez SC, Fang RF, Shipman SL -
Limitations of fluorescent timer protein maturation kinetics to isolate transcriptionally synchronized cortically differentiating human pluripotent stem cells.
bioRxiv : the preprint server for biology 2023 Peter M, Shipman S, Macklis JD -
A High-Throughput Colocalization Pipeline for Quantification of Mitochondrial Targeting across Different Protein Types.
ACS synthetic biology 2023 Lear SK, Nunez JA, Shipman SL -
Simultaneous multi-site editing of individual genomes using retron arrays.
bioRxiv : the preprint server for biology 2023 González-Delgado A, Lopez SC, Rojas-Montero M, Fishman CB, Shipman SL -
Temporally resolved transcriptional recording in E. coli DNA using a Retro-Cascorder.
Nature protocols 2023 Lear SK, Lopez SC, González-Delgado A, Bhattarai-Kline S, Shipman SL -
High-throughput colocalization pipeline quantifies efficacy of mitochondrial targeting signals across different protein types.
bioRxiv : the preprint server for biology 2023 Lear SK, Nunez JA, Shipman SL -
Continuous Multiplexed Phage Genome Editing Using Recombitrons.
bioRxiv : the preprint server for biology 2023 Fishman CB, Crawford KD, Bhattarai-Kline S, Zhang K, González-Delgado A, Shipman SL -
Molecular recording: transcriptional data collection into the genome.
Current opinion in biotechnology 2022 Lear SK, Shipman SL -
Recording gene expression order in DNA by CRISPR addition of retron barcodes.
Nature 2022 Bhattarai-Kline S, Lear SK, Fishman CB, Lopez SC, Lockshin ER, Schubert MG, Nivala J, Church GM, Shipman SL -
Retron reverse transcriptase termination and phage defense are dependent on host RNase H1.
Nucleic acids research 2022 Palka C, Fishman CB, Bhattarai-Kline S, Myers SA, Shipman SL -
Precise genome editing across kingdoms of life using retron-derived DNA.
Nature chemical biology 2021 Lopez SC, Crawford KD, Lear SK, Bhattarai-Kline S, Shipman SL -
Characterizing the portability of phage-encoded homologous recombination proteins.
Nature chemical biology 2021 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 -
Spontaneous CRISPR loci generation in vivo by non-canonical spacer integration.
Nature microbiology 2018 Nivala J, Shipman SL, Church GM -
The cellular and molecular landscape of neuroligins.
Trends in neurosciences 2015 Bemben MA, Shipman SL, Nicoll RA, Roche KW -
Rapid neurogenesis through transcriptional activation in human stem cells.
Molecular systems biology 2014 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 -
CaMKII phosphorylation of neuroligin-1 regulates excitatory synapses.
Nature neuroscience 2013 Bemben MA, Shipman SL, Hirai T, Herring BE, Li Y, Badger JD, Nicoll RA, Diamond JS, Roche KW -
Distance-dependent scaling of AMPARs is cell-autonomous and GluA2 dependent.
The Journal of neuroscience : the official journal of the Society for Neuroscience 2013 Shipman SL, Herring BE, Suh YH, Roche KW, Nicoll RA -
Dimerization of postsynaptic neuroligin drives synaptic assembly via transsynaptic clustering of neurexin.
Proceedings of the National Academy of Sciences of the United States of America 2012 Shipman SL, Nicoll RA -
A subtype-specific function for the extracellular domain of neuroligin 1 in hippocampal LTP.
Neuron 2012 Shipman SL, Nicoll RA -
Functional dependence of neuroligin on a new non-PDZ intracellular domain.
Nature neuroscience 2011 Shipman SL, Schnell E, Hirai T, Chen BS, Roche KW, Nicoll RA -
Absence of established sex differences in patients with schizophrenia on a two-dimensional object array task.
Psychiatry research 2009 Shipman SL, Baker EK, Pearlson G, Astur RS -
Factors affecting the hippocampal BOLD response during spatial memory.
Behavioural brain research 2007 Shipman SL, Astur RS