Seth Shipman, PhD

Assistant Professor

Department of Bioengineering and Therapeutic Sciences

[email protected]

Phone: +1 415 734-4058

1650 Owens Street

UCSF Box 1230

San Francisco, CA 94158

United States

Links

Shipman Lab

UCSF Profiles

Joint appointments

Assistant 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

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

Space Perception, Genome, Bacterial, CRISPR-Cas Systems, PDZ Domains, biotechnology, Cell Adhesion Molecules, Neuronal, Motion Pictures, Pyramidal Cells, Receptors, AMPA, CA1 Region, Hippocampal, Nerve Tissue Proteins, Gene Editing, synthetic biology, Clustered Regularly Interspaced Short Palindromic Repeats, Hippocampus

1.	The SN 10: Scientists to Watch, ScienceNews, 2019
2.	Bridge to Indipendence Award, Simonds Foundation Autism Research Initiative (SFARI), 2019
3.	DARPA Riser, DARPA 60th Anniversity Symposium, DARPA, 2018
4.	Postdoctoral Award, Life Science Research Foundation, 2014
5.	Travel Award, Earle C. Anthony, 2012
6.	Poster Award, Gordon Research Conference, 2012
7.	Grass Fellowship in Neuroscience (declined), Grass Foundation, 2011
8.	Graduate Research Fellowship, Honorable Mention, National Science Foundation, 2007-2008
9.	Outstanding Physics Student Scholarship, Wesleyan University, 2001

Publications

Bhattarai-Kline S, Lear SK, Shipman SL. One-step data storage in cellular DNA. Nat Chem Biol. 2021 Jan 26.

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 Jan 18.

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. 2020 Nov 30.

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.

Molecular recordings by directed CRISPR spacer acquisition. Science. 2016 Jul 29; 353(6298):aaf1175.

The cellular and molecular landscape of neuroligins. Trends Neurosci. 2015 Aug; 38(8):496-505.

Rapid neurogenesis through transcriptional activation in human stem cells. Mol Syst Biol. 2014 Nov 17; 10:760.

CaMKII phosphorylation of neuroligin-1 regulates excitatory synapses. Nat Neurosci. 2014 Jan; 17(1):56-64.

Distance-dependent scaling of AMPARs is cell-autonomous and GluA2 dependent. J Neurosci. 2013 Aug 14; 33(33):13312-9.

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.

A subtype-specific function for the extracellular domain of neuroligin 1 in hippocampal LTP. Neuron. 2012 Oct 18; 76(2):309-16.

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.