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An experimental census of retrons for DNA production and genome editing

bioRxiv (2024)

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

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

bioRxiv (2024)

Lopez SC, Lee Y, Zhang K, Shipman SL

Simultaneous multi-site editing of individual genomes using retron arrays

Nature Chemical Biology (in press)

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

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

bioRxiv (2024)

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

Limitations of fluorescent timer protein maturation kinetics to isolate transcriptionally synchronized cortically differentiating human pluripotent stem cells

bioRxiv (2023)

Peter M, Shipman SL, Macklis JD

Continuous Multiplexed Phage Genome Editing Using Recombitrons

bioRxiv (2023)

Fishman CB*, Crawford KD*, Bhattarai-Kline S*, Zhang KA, González-Delgado A, Shipman SL.

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.

Nature Microbiology (2018)

Nivala J, Shipman SL, Church GM.

Coverage: News & Views

CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria.
Molecular recordings by directed CRISPR spacer acquisition.
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.

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