Gladstone Institutes & UCSF
Genome editing of phylogenetically distinct bacteria using portable retron-mediated recombineering
bioRxiv (2025)
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 V, van Pijkeren JP, Shipman SL
Phage defense and genome editing using novel retrons sourced from isolated environmental bacteria
bioRxiv (2025)
Nakamura KL*, Zhang K*, Mestre MR, Rojas-Montero M, 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
High throughput variant libraries and machine learning yield design rules for retron gene editors
Nucleic Acids Research (2024)
Crawford KD, Khan AG, Lopez SC, Goodarzi H, Shipman SL
Continuous Multiplexed Phage Genome Editing Using Recombitrons
Nature Biotechnology (2024)
Fishman CB*, Crawford KD*, Bhattarai-Kline S*, Poola D*, Zhang KA, González-Delgado A, Rojas-Montero M, Shipman SL
free full-text here
Coverage: Nature Biotechnology, GEN, The Microbiologist, World News Today, MedIndia, From Bench to Podcast
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
free full-text here
Coverage: Cell Chemical Biology Spotlight
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.
free full-text here
Coverage: Phys.org
Directed differentiation of functional corticospinal-like neurons from endogenous SOX6+/NG2+ cortical progenitors
eLife (2024)
Ozkan A, Padmanabhan HK, Shipman SL, Azim E, Kumar P, Sadegh C, Basak AN, Macklis JD.
Coverage: eLife Magazine
Limitations of fluorescent timer protein maturation kinetics to isolate transcriptionally synchronized human neural progenitor cells
iScience (2024)
Peter M, Shipman SL, Heo J, 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.
Temporally resolved transcriptional recordings into E. coli DNA using a Retro-Cascorder
Nature Protocols (2023)
Lear SK*, Lopez SC*, González-Delgado A, Bhattarai-Kline S, Shipman SL.
Molecular recording: transcriptional data collection into the genome
Current Opinion in Biotechnology (2023)
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 E, Schubert MG, Nivala J, Church G, Shipman SL.
Coverage: Wired, Nature Methods, Spectrum
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 (2022)
Lopez SC, Crawford KD, Lear SK, Bhattarai-Kline S, Shipman SL.
Coverage: Scientific American
High throughput functional variant screens via in-vivo production of single-stranded DNA
PNAS (2021)
Schubert MG, Goodman DB, Wannier TM, Kaur D, Farzadfard F, Lu TK, Shipman SL, Church GM.
One-step data storage in cellular DNA
Nature Chemical Biology (2021)
Bhattarai-Kline S, Lear SK, 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.
A comprehensive library of human transcription factors for cell fate engineering
Nature Biotechnology (2020)
Ng AHM, Khoshakhlagh P, Arias JER, Pasquini G, Wang K, Anka S, 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.
CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria.
Nature (2017)
Shipman SL, Nivala J, Macklis JD, Church GM.
Coverage: NIH Director's Blog, Nature News, The New York Times, The Atlantic, MIT Technology Review, The Los Angeles Times, The Guardian, Discover Top Stories of 2017
Molecular recordings by directed CRISPR spacer acquisition.
Science (2016)
Shipman SL*, Nivala J*, Macklis JD, Church GM.
Coverage: Cell Systems: Principles of Systems Biology, Science: Perspective, Synthetic Biology, Gizmodo, Popular Mechanics, The Scientist
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 AHM, Shipman SL, Byrne S, Sanjana NE, Murn J, Li Y, Li S, Stadler M, Weiss R, Church GM.
Rosetta Brains: A Strategy for Molecularly-Annotated Connectomics.
arXiv (2014)
Marblestone AH, Daugharthy ER, Kalhor R, Peikon ID, Kebschull JM, Shipman SL, Mishchenko Y, Lee JH, Kording KP, Boyden ES, Zador AM, Church GM.
CaMKII phosphorylation of neuroligin-1 regulates excitatory synapses.
Nature Neuroscience (2014)
Bemben MA, Shipman SL, Hirai T, Herring BE, Li Y, Badger JD, Nicoll RA, Diamond JS, Roche KW.
Conneconomics: The Economics of Dense, Large-Scale, High-Resolution Neural Connectomics.
bioRxiv (2013)
Marblestone AH, Daugharthy ER, Kalhor R, Peikon ID, Kebschull JM, Shipman SL, Mishchenko Y, Lee JH, Dalrymple DA, Zamft BM, Kording KP, Boyden ES, Zador AM, Church GM.
Distance dependent scaling of AMPARs is cell-autonomous and GluA2-dependent.
The Journal of Neuroscience (2013)
Shipman SL, Herring BE, Suh YH, Roche KW, Nicoll RA.
Dimerization of postsynaptic neuroligin drives synaptic assembly via transsynaptic clustering of neurexin.
Proc Natl Acad Sci USA (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.
Coverage: F1000 Recommended Article
Absence of established sex differences in patients with schizophrenia on a 2-dimensional object array task.
Psychiatry Research (2009)
Shipman SL,Baker EK, Pearlson GD, Astur RS.
Factors affecting the hippocampal BOLD response during fMRI: Activation versus deactivation.
Behavioral Brain Research (2008)
Shipman SL, Astur RS.