Seth Shipman, PhD

Assistant Professor

Department of Bioengineering and Therapeutic Sciences

[email protected]

Phone: +1 415 734-4058

Links

Shipman Lab UCSF Profiles Gladstone Institutes

Affiliations

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

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
Information Storage and Retrieval
biotechnology
DNA
Cell Adhesion Molecules, Neuronal
Motion Pictures
E. coli
Reverse Transcription
Nerve Tissue Proteins
Gene Editing
synthetic biology
Bacteriophages
Clustered Regularly Interspaced Short Palindromic Repeats

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

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.