Seth Shipman, PhD
Associate Professor
Bioengineering
School of Pharmacy

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.

• High throughput variant libraries and machine learning yield design rules for retron gene editors.
  Nucleic acids research 2025 Crawford KD, Khan AG, Lopez SC, Goodarzi H, Shipman SL
• SspA is a transcriptional regulator of CRISPR adaptation in E. coli.
  Nucleic acids research 2024 Lopez SC, Lee Y, Zhang K, Shipman SL
• An experimental census of retrons for DNA production and genome editing.
  Nature biotechnology 2024 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 2024 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 2024 Crawford KD, Khan AG, Lopez SC, Goodarzi H, Shipman SL
• Simultaneous multi-site editing of individual genomes using retron arrays.
  Nature chemical biology 2024 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 2024 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 2024 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 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