Publications

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Zernicka-Goetz M, Morris SA, Bruce AW. Nat Rev Genet. 2009

Morris et al., Cahan et al., Cell. 2014

Kong et al., Cell Stem Cell. 2022

Papers

Kunal Jindal, Mohd Tayyab Adil, Naoto Yamaguchi, Xue Yang, Helen C. Wang, Kenji Kamimoto, Guillermo C. Rivera-Gonzalez, and Samantha A. Morris.
Single-cell lineage capture across genomic modalities with CellTag-multi reveals fate-specific gene regulatory changes.
Nature Biotechnol. 2024 Jun;42(6):946-959. doi: 10.1038/s41587-023-01931-4

Guillermo C. Rivera-Gonzalez, Emily G. Butka, Carolynn E. Gonzalez, Wenjun Kong, Kunal Jindal, and Samantha A. Morris
Single-cell lineage tracing reveals hierarchy and mechanism of adipocyte precursor maturation.
BioRxiv. 2023 Jun 4; https://doi.org/10.1101/2023.06.01.543318

Junedh M. Amrute, Lulu Lai, Pan Ma, Andrew L. Koenig, Kenji Kamimoto, Andrea Bredemeyer, Thirupura S. Shankar, Christoph Kuppe, Farid F. Kadyrov, Linda J. Schulte, Dylan Stoutenburg, Benjamin J. Kopecky, Sutip Navankasattusas, Joseph Visker, Samantha A. Morris, Rafael Kramann, Florian Leuschner, Douglas L. Mann, Stavros G. Drakos, and Kory J. Lavine.
Defining cardiac functional recovery in end-stage heart failure at single-cell resolution.
Nature Cardiovasc Res. 2023 Apr; 2(4): 399–416.

Kenji Kamimoto, Blerta Stringa, Christy M. Hoffmann, Kunal Jindal, Lila Solnica-Krezel, Samantha A. Morris.
Dissecting cell identity via network inference and in silico gene perturbation.
Nature. 2023 Feb 8. doi: 10.1038/s41586-022-05688-9.

News and Views: An oracle predicts regulators of cell identity.

Research Highlight: Single-cell analysis enters the multiomics age.

Kenji Kamimoto, Mohd Tayyab Adil, Kunal Jindal, Christy M. Hoffmann, Wenjun Kong, Xue Yang, Samantha A. Morris.
Gene regulatory network reconfiguration in direct lineage reprogramming.
Stem Cell Reports 2023 January 11; 10;18(1):97-112. doi: 10.1016/j.stemcr.2022.11.010.

Kunal Jindal, Mohd Tayyab Adil, Naoto Yamaguchi, Helen C. Yang, Kenji Kamimoto, Guillermo C. Rivera-Gonzalez, Samantha A. Morris.
Multiomic single-cell lineage tracing to dissect fate-specific gene regulatory programs.
BioRxiv 2022 October 24; doi: https://doi.org/10.1101/2022.10.23.512790

Stephanie A. Luff , J. Philip Creamer, Sara Valsoni, Carissa Dege, Rebecca Scarfò, Analisa Dacunto, Sara Cascione, Lauren N. Randolph, Eleonora Cavalca, Ivan Merelli, Samantha A. Morris, Andrea Ditadi, Christopher M. Sturgeon.
Identification of a retinoic acid-dependent haemogenic endothelial progenitor from human pluripotent stem cells
Nature Cell Biology 2022 May 24; doi:0.1038/s41556-022-00898-9

Wenjun Kong, Yuheng C. Fu, Emily M. Holloway, Gorkem Garipler, Xue Yang, Esteban Mazzoni, Samantha A. Morris.
Capybara: A computational tool to measure cell identity and fate transitions.
Cell Stem Cell 2022 Mar 29; doi: https://doi.org/10.1016/j.stem.2022.03.001

Kunal Jindal, Sadie VanHorn, Samantha A Morris.
New dual-channel system records lineage in high definition.
Nat Methods. 2022 Jan;19(1):38-39.

Kangyun Wu, Kenji Kamimoto, Yong Zhang, Kuangying Yang, Shamus P Keeler, Benjamin J Gerovac, Eugene V Agapov, Stephen P Austin, Jennifer Yantis, Kelly A Gissy, Derek E Byers, Jennifer Alexander-Brett, Christy M Hoffmann, Matthew Wallace, Michael E Hughes, Erika C Crouch, Samantha A Morris, Michael J Holtzman.
Basal epithelial stem cells cross an alarmin checkpoint for postviral lung disease.
J Clin Invest. 2021 Aug 10:149336.

Vittoria Dickinson Bocchi, Paola Conforti, Elena Vezzoli, Dario Besusso, Claudio Cappadona, Tiziana Lischetti,
Maura Galimberti, Valeria Ranzani, Raoul J. P. Bonnal, Marco De Simone, Grazisa Rossetti, Xiaoling He,
Kenji Kamimoto, Ira Espuny-Camacho, Andrea Faedo, Federica Gervasoni, Romina Vuono, Samantha A. Morris,
Jian Chen, Dan Felsenfeld, Giulio Pavesi, Roger A. Barker, Massimiliano Pagani, Elena Cattaneo.
The coding and long noncoding single-cell atlas of the developing human fetal striatum.
Science. 2021 May 7;372(6542):eabf5759. doi: 10.1126/science.abf5759.

Research Highlight: Single-cell analysis enters the multiomics age.

Kyaw Thu Minn, Sabine Dietmann, Sarah E Waye, Samantha A Morris, Lilianna Solnica-Krezel
Gene expression dynamics underlying cell fate emergence in 2D micropatterned human embryonic stem cell gastruloids.
Stem Cell Reports. 2021 May 11;16(5):1210-1227. doi: 10.1016/j.stemcr.2021.03.031.

Dana Klatt Shaw, Vishnu Muraleedharan Saraswathy, Lili Zhou, Anthony R McAdow, Brooke Burris, Emily Butka, Samantha A Morris, Sabine Dietmann, and Mayssa H Mokalled.
Localized EMT reprograms glial progenitors to promote spinal cord repair.
Developmental Cell. 2021 Mar 8;56(5):613-626.e7. doi: 10.1016/j.devcel.2021.01.017.

Sadie VanHorn and Samantha A. Morris.
Next-generation lineage tracing and fate mapping to interrogate development.
Developmental Cell. 2021 Jan 11;56(1):7-21. doi: 10.1016/j.devcel.2020.10.021.

Owen Rackham, Patrick Cahan, Nancy Mah, Samantha Morris, John F. Ouyang, Anne L. Plant, Yoshiaki Tanaka, Christine A. Wells
Challenges for Computational Stem Cell Biology: A Discussion for the Field
Stem Cell Reports. 2021 Jan 12;16(1):3-9. doi: 10.1016/j.stemcr.2020.12.015.

Patrick Cahan, Davide Cacchiarelli, Sara-Jane Dunn, Martin Hemberg, Susana M Chuva de Sousa Lopes, Samantha A. Morris, Owen J.L. Rackham, Antonio Del Sol, and Christine A. Wells.
Computational Stem Cell Biology: Open Questions and Guiding Principles.
Cell Stem Cell. 2021 Jan 7;28(1):20-32. doi: 10.1016/j.stem.2020.12.012.

Kyaw T. Minn, Yuheng C. Fu, Shenghua He, Sabine Dietmann, Stephen C. George, Mark C. Anastasio, Samantha A. Morris*, Lila Solnica-Krezel*.
High-resolution transcriptional and morphogenetic profiling of cells from micropatterned human ESC gastruloid cultures.
Elife. 2020 Nov 18;9:e59445. doi: 10.7554/eLife.59445. *co-senior authors

Kitra Cates, Matthew J. McCoy, Ji-Sun Kwon, Yangjian Liu, Daniel G. Abernathy, Bo Zhang, Shaopeng Liu, Paul Gontarz, Woo Kyung Kim, Shawei Chen, Wenjun Kong, Joshua N. Ho, Kyle F. Burbach, Harrison W. Gabel, Samantha A. Morris, and Andrew S. Yoo.
Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs
Cell Stem Cell 2020 September 21; https://doi.org/10.1016/j.cell.2020.06.037.

Yanan Li**, Wenjun Kong**, Wei Yang, Riddhi M. Patel, Emily B. Casey, Theresa Okeyo-Owuor, J. Michael White,
Shaina N. Porter, Samantha A. Morris*, and Jeffrey A. Magee*
Single-Cell Analysis of Neonatal HSC Ontogeny Reveals Gradual and Uncoordinated Transcriptional Reprogramming that Begins before Birth
Cell Stem Cell 2020 August 20; https://doi.org/10.1016/j.cell.2020.06.037. *co-senior authors, **co-first authors

Arnav Moudgil, Michael N. Wilkinson, Xuhua Chen, June He, Alexander J. Cammack, Michael J. Vasek, Tomas Lagunas, Jr., Zongtai Qi, Matthew A. Lalli, Chuner Guo, Samantha A. Morris, Joseph D. Dougherty, and Robi D. Mitra
Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells
Cell 2020 August 20; https://doi.org/10.1016/j.cell.2020.06.037

Kenji Kamimoto, Christy M. Hoffmann, Samantha A. Morris.
CellOracle: Dissecting cell identity via network inference and in silico gene perturbation
BioRxiv 2020 Feb 18; doi: https://doi.org/10.1101/2020.02.17.947416

News and Views: An oracle predicts regulators of cell identity.

Research Highlight: Single-cell analysis enters the multiomics age.

Wenjun Kong, Yuheng C. Fu, Samantha A. Morris.
Capybara: A computational tool to measure cell identity and fate transitions.
BioRxiv 2020 Feb 18; doi: https://doi.org/10.1101/2020.02.17.947390

Wenjun Kong, Brent A. Biddy, Kenji Kamimoto, Junedh M. Amrute, Emily G. Butka, Samantha A. Morris.
CellTagging: combinatorial indexing to simultaneously map lineage and identity at single-cell resolution.
Nature Protocols 2020 Feb 12; doi: 10.1038/s41596-019-0247-2.

Kyaw Thu Minn, Yuheng C. Fu, Shenghua He, Steven C. George, Mark A. Anastasio, Samantha A. Morris*, Lilianna Solnica-Krezel*. *co-senior authors.
High-resolution transcriptional and morphogenetic profiling of cells from micropatterned human embryonic stem cell gastruloid cultures.
BioRxiv 2020 Jan;915777. doi: https://doi.org/10.1101/2020.01.22.915777

Samantha A. Morris.
Cell identity reprogrammed.
Nature. 2019 Nov;575(7781):44-45. doi: 10.1038/d41586-019-02834-8.

Kristen M. Seiler*, Sarah E. Waye*, Wenjun Kong, Kenji Kamimoto, Adam Bajinting, William H. Goo, Emily J. Onufer, Cathleen Courtney, Jun Guo, Brad W. Warner1**, Samantha A. Morris**. *co-first; **co-corresponding.
Single-Cell Analysis Reveals Regional Reprogramming during Adaptation to Massive Small Bowel Resection in Mice
Cellular and Molecular Gastroenterology and Hepatology. 2019;8(3):407-426. doi: 10.1016/j.jcmgh.2019.06.001.

Samantha A. Morris.
The evolving concept of cell identity in the single cell era.
Development. 2019 Jun 27;146(12).

Chuner Guo, Wenjun Kong, Kenji Kamimoto, Guillermo. C. Rivera-Gonzalez, Xue Yang, Yuhei Kirita, Samantha A. Morris
CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics.
Genome Biology. 2019 May;9;20(1):90. doi: 10.1186/s13059-019-1699-y.

Samantha A. Morris.
Pinpointing a spatial address for RNA profiles in tissues.
Nature. 2019 May;569(7755):197-199. doi: 10.1038/d41586-019-01405-1.

Kristen M. Seiler*, Sarah E. Waye*, Wenjun Kong, Kenji Kamimoto, Adam Bajinting, William H. Goo, Emily J. Onufer, Cathleen Courtney, Jun Guo, Brad W. Warner1**, Samantha A. Morris**. *co-first; **co-corresponding.
Single-Cell Analysis Reveals Regional Reprogramming during Adaptation to Massive Small Bowel Resection in Mice
BioRxiv. 2019 Apr; https://www.biorxiv.org/content/10.1101/615054v1.

Arnav Moudgil, Michael N. Wilkinson, Xuhua Chen, June He, Alex J. Cammack, Michael J.
Vasek, Tomas Lagunas, Jr., Zongtai Qi, Samantha A. Morris, Joseph D. Dougherty, Robi D. Mitra.
Self-reporting transposons enable simultaneous readout of gene expression and transcription factor binding in single cells.
BioRxiv. 2019 Feb 20; https://www.biorxiv.org/content/10.1101/538553v2

Brent A. Biddy, Wenjun Kong, Kenji Kamimoto, Chuner Guo, Sarah E. Waye, Tao Sun & Samantha A. Morris.
Single-cell mapping of lineage and identity in direct reprogramming.
Nature. 2018 Dec 13; 564(7735):219-224. doi: 10.1038/s41586-018-0744-4.

Research Highlight: Tagged reprogramming.

Blog post: Single-cell mapping of lineage and identity in direct reprogramming.

Wenjun Kong & Samantha A. Morris.
Evaluation of Wu et al.: Comprehending Global and Local Structure of Single-Cell Datasets.
Cell Systems. 2018 Dec 26;7(6):565-566. doi: 10.1016/j.cels.2018.12.003.

Guillermo C. Rivera-Gonzalez & Samantha A. Morris.
Tracing the Origins of Axolotl Limb Regeneration.
Developmental Cell. 2018 Dec 17; 47(6):675-677. doi: 10.1016/j.devcel.2018.11.042.

Haojia Wu, Kohei Uchimura, Erinn Donnelly, Yuhei Kirita, Samantha A Morris, Benjamin D Humphreys.
Comparative Analysis and Refinement of Human PSC-Derived Kidney Organoid Differentiation with Single-Cell Transcriptomics.
Cell Stem Cell. 2018 Nov 15; doi: https://doi.org/10.1016/j.stem.2018.10.010

Chuner Guo, Brent A Biddy, Kenji Kamimoto, Wenjun Kong, Samantha A Morris
CellTag Indexing: a genetic barcode-based multiplexing tool for single-cell technologies
BioRxiv. 2018 May 31; doi: https://doi.org/10.1101/127860

Kenji Kamimoto and Samantha A Morris.

Breaking New Ground in the Landscape of Single-Cell Analysis.

Cell Systems. 2018 Jan 24;6(1):5-7. doi: 10.1016/j.cels.2017.12.015.

Haojia Wu, Kohei Uchimura, Erinn Donnelly, Yuhei Kirita, Samantha A Morris, Benjamin D Humphreys

Comparative analysis of kidney organoid and adult human kidney single cell and single nucleus transcriptomes.

BioRxiv. 2017 Dec 11; doi: https://doi.org/10.1101/232561

Guo C and Morris SA.

Engineering cell identity: establishing new gene regulatory and chromatin landscapes.

Curr Opin Genet Dev. 2017 Jun 28;46:50-57. doi: 10.1016/j.gde.2017.06.011.

Biddy BA, Waye SE, Sun T, Morris SA.

Single-cell analysis of clonal dynamics in direct lineage reprogramming: a combinatorial indexing method for lineage tracing.

BioRxiv. 2017 Apr; doi: https://doi.org/10.1101/127860

Morris SA.

Human embryos cultured in vitro to 14 days.

Open Biology. 2017 Jan;7(1). pii: 170003. doi: 10.1098/rsob.170003

Morris SA.

Direct lineage reprogramming via pioneer factors; a detour through developmental gene regulatory networks.

Development. 2016 143: 2696-2705; doi: 10.1242/dev.138263.

Morris SA.

Single-Cell RNA-Seq Steps Up to the Growth Plate.

Trends Biotechnol. 2016; 34(7):525-7.

Diaz MF, Li N, Lee HJ, Adamo L, Evans SM, Willey HE, Arora N, Torisawa YS, Vickers DA, Morris SA, Naveiras O, Murthy SK, Ingber DE, Daley GQ, García-Cardeña G, Wenzel PL.

Biomechanical forces promote blood development through prostaglandin E2 and the cAMP-PKA signaling axis.

J Exp Med. 2015 May 4;212(5):665-80.

Cahan P, Morris SA, Collins JJ, Daley GQ.

Defining cellular identity through network biology.

Cell Cycle. 2014 Nov 14;13(21):3313-14

Morris SA*, Cahan PC*, Li H*, Zhao A, San Roman AK, Shivdasani RA, Collins JJ, Daley GQ.

Dissecting Engineered Cell Types and Enhancing Cell Fate Conversion via CellNet.

Cell. 2014 Aug 14;158(4):889-902. * Equal contribution. Featured on cover

Cell commentary: CellNet–where your cells are standing

Nature commentary: Network biology: A compass for stem-cell differentiation

Nature Biotechnology commentary: A blueprint of cell identity

Cahan PC*, Li H*, Morris SA*, Lummertz da Rocha E, Daley GQ, Collins JJ.

CellNet: Network Biology Applied to Stem Cell Engineering.

Cell. 2014 Aug 14;158(4):903-15. * Equal contribution. Featured on cover

Cell commentary: CellNet–where your cells are standing

Nature commentary: Network biology: A compass for stem-cell differentiation

Nature Biotechnology commentary: A blueprint of cell identity

Fgf signalling in the pre-implantation embryo

Morris SA, Graham SJ, Jedrusik A, Zernicka-Goetz M.

The differential response to Fgf signalling in cells internalized at different times influences lineage segregation in preimplantation mouse embryos.

Open Biol. 2013 Nov20;3(11):130104

Featured on cover

Morris SA, Daley GQ.

A blueprint for engineering cell fate: current technologies to reprogram cell identity.

Cell Res. 2013 Jan;23(1):33-48. Review

Winner of The 2013 Sanofi-Cell Research Outstanding Review Article Award

Jones MR, Blahna MT, Kozlowski E, Matsuura KY, Ferrari JD, Morris SA, Powers JT, Daley GQ, Quinton LJ, Mizgerd JP.

Zcchc11 uridylates mature miRNAs to enhance neonatal IGF-1 expression, growth, and survival.

PLoS Genet. 2012;8(11)

Fgf and Wnt signalling in pre-implantation mouse embryo

Morris SA, Gu Y, and Zernicka-Goetz M.

Developmental plasticity is bound by pluripotency and the Fgf and Wnt signaling pathways.

Cell Reports. 2012. Oct 25;2(4):756-65

Featured among Cell Reports’ Best of 2012

In vitro implantation of the developing embryo

Morris SA*, Grewal S*, Barrios F*, Patankar SN, Strauss B, Buttery L, Alexander M, Shakesheff K and Zernicka Goetz M.

Dynamics of anterior-posterior axis formation in the developing mouse embryo.

Nature Commun. 2012 Feb 14;3:673. * Equal contribution

Science Daily News Article

Morris SA.

Reply: Cell fate in the early mouse embryo: Sorting out the influence of developmental history on lineage choice.

Reprod Biomed Online. 2011 Jun;22(6):521-4

Morris SA.

Cell fate in the early mouse embryo: Sorting out the influence of developmental history on lineage choice.

Reprod Biomed Online. 2011 Jun;22(6):521-4

Origin of the first lineages of the mouse embryo

Morris SA, Teo RT, Li H, Robson P, Glover DM, Zernicka-Goetz M.

Origin and formation of the first two distinct cell types of the inner cell mass in the mouse embryo.

Proc Natl Acad Sci USA. 2010 Apr 6;107(14):6364-9

Review of early developmental patterning

Zernicka-Goetz M, Morris SA, Bruce AW.

Making a firm decision: multifaceted regulation of cell fate in the early mouse embryo.

Nat Rev Genet. 2009 Jul;10(7):467-77. Review

Featured on cover

Meilhac SM, Adams RJ*, Morris SA*, Danckaert A, Le Garrec JF, Zernicka-Goetz M.

Active cell movements coupled to positional induction are involved in lineage segregation in the mouse blastocyst.

Dev Biol. 2009 Jul 15;331(2):210-21. * Equal contribution

Morris SA, Almeida AD, Tanaka H, Ohta K, Ohnuma S.

Tsukushi modulates Xnr2, FGF and BMP signaling: regulation of Xenopus germ layer formation.

PLoS One. 2007 Oct 10;2(10):e1004

Harrington AE, Morris SA, Ruotolo BT, Robinson CV, Ohnuma S, Hyvonen M.

Structural basis for the inhibition of activin signalling by follistatin.

EMBO J. 2006 Mar 8;25(5):1035-45.

Anderson AA, Kendal CE, Garcia-Maya M, Kenny AV, Morris SA, Wu T, Reynolds R, Hohenester E, Saffell JL.

A peptide from the first fibronectin domain of NCAM acts as an inverse agonist and stimulates FGF receptor activation, neurite outgrowth and survival.

J Neurochem. 2005 Oct;95(2):570-83