Seth Shipman, PhD

Assistant Professor
+1 415 734-4058

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.

Dr. Shipman is an Assistant Professor in the Department of Bioengineering and Therapeutic Sciences at UCSF and an Assistant Investigator in the Gladstone Institute of Data Science and Biotechnology. He received his undergraduate degree in Neuroscience from Wesleyan University, his PhD in Neuroscience from UCSF, and completed his postdoctoral training at Harvard Medical School with George Church and Jeffrey Macklis. His postdoctoral work was in the top 30 most discussed articles of the year as ranked by Altmetric and was named as one of the top 25 stories of the year by Discover Magazine. He was a Shurl and Kay Curci Foundation Fellow of the Life Sciences Research Foundation, received a Bridge to Independence Award from the Simons Foundation Autism Research Initiative, and was recently named a DARPA Riser and one of 10 early- to mid-career scientists to watch by Science News (the SN10).

Simultaneous multi-site editing of individual genomes using retron arrays.

bioRxiv : the preprint server for biology

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

Lear SK, Lopez SC, Gonz?lez-Delgado A, Bhattarai-Kline S, Shipman SL

Continuous Multiplexed Phage Genome Editing Using Recombitrons.

bioRxiv : the preprint server for biology

Fishman CB, Crawford KD, Bhattarai-Kline S, Zhang K, Gonz Lez-Delgado A, Shipman SL

Molecular recording: transcriptional data collection into the genome.

Current opinion in biotechnology

Lear SK, Shipman SL

Recording gene expression order in DNA by CRISPR addition of retron barcodes.


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

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

Lopez SC, Crawford KD, Lear SK, Bhattarai-Kline S, Shipman SL

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

One-step data storage in cellular DNA.

Nature chemical biology

Bhattarai-Kline S, Lear SK, Shipman SL

Characterizing the portability of phage-encoded homologous recombination proteins.

Nature chemical biology

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

A comprehensive library of human transcription factors for cell fate engineering.

Nature biotechnology

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

Spontaneous CRISPR loci generation in vivo by non-canonical spacer integration.

Nature microbiology

Nivala J, Shipman SL, Church GM

Molecular recordings by directed CRISPR spacer acquisition.

Science (New York, N.Y.)

Shipman SL, Nivala J, Macklis JD, Church GM

The cellular and molecular landscape of neuroligins.

Trends in neurosciences

Bemben MA, Shipman SL, Nicoll RA, Roche KW

Rapid neurogenesis through transcriptional activation in human stem cells.

Molecular systems biology

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

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

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

Shipman SL, Nicoll RA

Functional dependence of neuroligin on a new non-PDZ intracellular domain.

Nature neuroscience

Shipman SL, Schnell E, Hirai T, Chen BS, Roche KW, Nicoll RA

Factors affecting the hippocampal BOLD response during spatial memory.

Behavioural brain research

Shipman SL, Astur RS