Seth Shipman, PhD | Health Innovation via Engineering

Assistant Professor

Bioengineering

+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).

Publications

MitoScribe single-cell molecular recorder logs graded signaling dynamics into mitochondrial DNA.

bioRxiv : the preprint server for biology

Wang L, Poulis N, Srivastava D, Shipman SL

Genome editing of phylogenetically distinct bacteria using portable retron-mediated recombineering.

bioRxiv : the preprint server for biology

González-Delgado A, Bonillo-Lopez L, Johnson MS, Knödlseder N, Ko CC, Lekbach Y, Oh JH, Selvakumar H, Wold MC, Yu Z, Aragón V, Gralnick JA, Güell M, Hatfull GF, Keitz BK, Koskella B, Mutalik VK, van Pijkeren JP, Shipman SL

SspA is a transcriptional regulator of CRISPR adaptation in E. coli.

Nucleic acids research

Lopez SC, Lee Y, Zhang K, Shipman SL

High throughput variant libraries and machine learning yield design rules for retron gene editors.

Nucleic acids research

Crawford KD, Khan AG, Lopez SC, Goodarzi H, Shipman SL

An experimental census of retrons for DNA production and genome editing.

Nature biotechnology

Khan AG, Rojas-Montero M, González-Delgado A, Lopez SC, Fang RF, Crawford KD, Shipman SL

Continuous multiplexed phage genome editing using recombitrons.

Nature biotechnology

Fishman CB, Crawford KD, Bhattarai-Kline S, Poola D, Zhang K, González-Delgado A, Rojas-Montero M, Shipman SL

High Throughput Variant Libraries and Machine Learning Yield Design Rules for Retron Gene Editors.

bioRxiv : the preprint server for biology

Crawford KD, Khan AG, Lopez SC, Goodarzi H, Shipman S

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

Nature chemical biology

González-Delgado A, Lopez SC, Rojas-Montero M, Fishman CB, Shipman SL

Limitations of fluorescent timer protein maturation kinetics to isolate transcriptionally synchronized human neural progenitor cells.

iScience

Peter M, Shipman S, Heo J, Macklis JD

Directed differentiation of functional corticospinal-like neurons from endogenous SOX6+/NG2+ cortical progenitors.

bioRxiv : the preprint server for biology

Ozkan A, Padmanabhan HK, Shipman SL, Azim E, Kumar P, Sadegh C, Basak AN, Macklis JD

An experimental census of retrons for DNA production and genome editing.

bioRxiv : the preprint server for biology

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

Peter M, Shipman S, Macklis JD

A High-Throughput Colocalization Pipeline for Quantification of Mitochondrial Targeting across Different Protein Types.

ACS synthetic biology

Lear SK, Nunez JA, Shipman SL

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

High-throughput colocalization pipeline quantifies efficacy of mitochondrial targeting signals across different protein types.

bioRxiv : the preprint server for biology

Lear SK, Nunez JA, 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.

Nature

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