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Author Details

Matt Thomson
California Institute of Technology
2009
40
18
Kirsten Obernier (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37131803D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response.bioRxiv2024
36736298Spin glasses, error correcting codes, and synchronization of human stem cell organoids.Cell2023
37697162Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references.Nat Methods2023
37650862Correction: A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice.Elife2023
37425903Configurational entropy is an intrinsic driver of tissue structural heterogeneity.bioRxiv2023
37425793Patterning and folding of intestinal villi by active mesenchymal dewetting.bioRxiv2023
37221392Author Correction: Stem cell-derived synthetic embryos self-assemble by exploiting cadherin codes and cortical tension.Nat Cell Biol2023
37314333Daily SARS-CoV-2 Nasal Antigen Tests Miss Infected and Presumably Infectious People Due to Viral Load Differences among Specimen Types.Microbiol Spectr2023
37168671Spatio-temporal patterning of extensile active stresses in microtubule-based active fluids.PNAS Nexus2023
36752605Motor processivity and speed determine structure and dynamics of microtubule-motor assemblies.Elife2023
34929723Reinforcement learning reveals fundamental limits on the mixing of active particles.Soft Matter2022
35679857Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments.Cell Syst2022
36100738Stem cell-derived synthetic embryos self-assemble by exploiting cadherin codes and cortical tension.Nat Cell Biol2022
35863345Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution.Cell Syst2022
36346385A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice.Elife2022
34301855A DNA repair pathway can regulate transcriptional noise to promote cell fate transitions.Science2021
34759919Deep Parallel Characterization of AAV Tropism and AAV-Mediated Transcriptional Changes <i>via</i> Single-Cell RNA Sequencing.Front Immunol2021
32965216Bimodal function of chromatin remodeler <i>Hmga1</i> in neural crest induction and Wnt-dependent emigration.Elife2020
31873215Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins.Nat Biotechnol2020
33303584Developmental clock and mechanism of de novo polarization of the mouse embryo.Science2020
33239690Single cell profiling of capillary blood enables out of clinic human immunity studies.Sci Rep2020
33127759Dissecting heterogeneous cell populations across drug and disease conditions with PopAlign.Proc Natl Acad Sci U S A2020
31391558Controlling organization and forces in active matter through optically defined boundaries.Nature2019
29395056Adult Neurogenesis Is Sustained by Symmetric Self-Renewal and Differentiation.Cell Stem Cell2018
30178802Integrated measurement of intracellular proteins and transcripts in single cells.Lab Chip2018
29414712Diffusion as a Ruler: Modeling Kinesin Diffusion as a Length Sensor for Intraflagellar Transport.Biophys J2018
27927684<i>In vitro</i> patterning of pluripotent stem cell-derived intestine recapitulates <i>in vivo</i> human development.Development2017
28591615Transient Thresholding: A Mechanism Enabling Noncooperative Transcriptional Circuitry to Form a Switch.Biophys J2017
26949256SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells.Elife2016
27825435Signaling Boundary Conditions Drive Self-Organization of Human "Gastruloids".Dev Cell2016
27135536Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing.Cell Syst2016
26830878Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors.Cell2016
25633040A strategy for tissue self-organization that is robust to cellular heterogeneity and plasticity.Proc Natl Acad Sci U S A2015
26405695Transcription factor competition allows embryonic stem cells to distinguish authentic signals from noise.Cell Syst2015
26050928Transcriptome-wide Analysis Reveals Hallmarks of Human Intestine Development and Maturation In Vitro and In Vivo.Stem Cell Reports2015
25254493Environmental statistics and optimal regulation.PLoS Comput Biol2014
21663792Pluripotency factors in embryonic stem cells regulate differentiation into germ layers.Cell2011
18647734Programming with models: modularity and abstraction provide powerful capabilities for systems biology.J R Soc Interface2009
19536158Unlimited multistability in multisite phosphorylation systems.Nature2009
19765594The rational parameterization theorem for multisite post-translational modification systems.J Theor Biol2009
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Collaborators

Magdalena Zernicka-Goetz
California Institute of Technology, USA. institute of technology.edu.
Co-authored papers 3
Jeremy Gunawardena
Harvard Medical School
Co-authored papers 3
Leor S Weinberger
Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes
Co-authored papers 2
Mark A LaBarge
Co-authored papers 2
Gregory Humphrey
University of California
Co-authored papers 2
Christopher K Glass
University of California San Diego
Co-authored papers 2
Tejal A Desai
University of California San Francisco
Co-authored papers 2
Wendell A Lim
University of California san francisco
Co-authored papers 1
Barbara Panning
University of California san francisco
Co-authored papers 1
Ravi V Desai
Gladstone Institutes
Co-authored papers 1
Rio Anderson
Co-authored papers 1
Peter J Dempsey
University of Colorado
Co-authored papers 1
Jos?? Manuel Garc??a-Verdugo
Cavanilles Institute, University of Valencia
Co-authored papers 1
Rob Knight
University of California
Co-authored papers 1
Robert A Coleman
Co-authored papers 1
Kirsten Obernier (CM4AI)
University of California San Francisco
Co-authored papers 1
Nilanjana Chatterjee
Chittaranjan National Cancer Institute
Co-authored papers 1
Alexander D Borowsky
University of California Davis Health
Co-authored papers 1
Jose L Rodas-Rodriguez
University of California-San Francisco
Co-authored papers 1
Hyunil Jo
Department of Pharmaceutical Chemistry, University of California San Francisco
Co-authored papers 1
James R Heath
Institute of Systems Biology, University of Washington
Co-authored papers 1
Lior Pachter
Co-authored papers 1
Arantxa Cebrian-Silla
University of California San Francisco
Co-authored papers 1
Alexander Meissner
Co-authored papers 1
Katherine S Pollard
Gladstone Institutes
Co-authored papers 1
Igor Antoshechkin
Co-authored papers 1
Jose I Parraguez
University of California san francisco
Co-authored papers 1
Cristina D Guinto
University of California-San Francisco
Co-authored papers 1
Arturo Alvarez-Buylla
University of California san francisco
Co-authored papers 1
William F DeGrado
Department of Pharmaceutical Chemistry, University of California san francisco
Co-authored papers 1
Release 1.2