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Author Details

Danielle L Swaney
J. David Gladstone Institutes
2007
83
36
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36711836Next-generation interaction proteomics for quantitative Jumbophage-bacteria interaction mapping.bioRxiv2023
37758692Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets.Nat Commun2023
37961561Multi-scale photocatalytic proximity labeling reveals cell surface neighbors on and between cells.bioRxiv2023
37858338High-throughput chemogenetic drug screening reveals PKC-RhoA/PKN as a targetable signaling vulnerability in GNAQ-driven uveal melanoma.Cell Rep Med2023
37857833A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response.Nat Cell Biol2023
38064566In vivo protein turnover rates in varying oxygen tensions nominate MYBBP1A as a mediator of the hyperoxia response.Sci Adv2023
37620325Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping.Nat Commun2023
38060380Molecular determinants of the crosstalk between endosomal microautophagy and chaperone-mediated autophagy.Cell Rep2023
37738983Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis.Cell Host Microbe2023
37738970SARS-CoV-2 variants evolve convergent strategies to remodel the host response.Cell2023
37645943The microenvironment dictates glycocalyx construction and immune surveillance.Res Sq2023
37577546Cross-family small GTPase ubiquitination by the intracellular pathogen <i>Legionella pneumophila</i>.bioRxiv2023
37873080Lysosomal proteomics reveals mechanisms of neuronal apoE4associated lysosomal dysfunction.bioRxiv2023
36993679Merlin<sup>S13</sup> phosphorylation controls meningioma Wnt signaling and magnetic resonance imaging features.Res Sq2023
37019383Quantitative Proteomic Analysis Reveals apoE4-Dependent Phosphorylation of the Actin-Regulating Protein VASP.Mol Cell Proteomics2023
37398395Deep learning from harmonized peptide libraries enables retention time prediction of diverse post translational modifications.bioRxiv2023
37398204CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis.bioRxiv2023
36692000Oncogenic PKA signaling increases c-MYC protein expression through multiple targetable mechanisms.Elife2023
35234472Data-Independent Acquisition Protease-Multiplexing Enables Increased Proteome Sequence Coverage Across Multiple Fragmentation Modes.J Proteome Res2022
35534562Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities.Nat Genet2022
36273492Resistance to ATR Inhibitors Is Mediated by Loss of the Nonsense-Mediated Decay Factor UPF2.Cancer Res2022
36116133Reduced endosomal microautophagy activity in aging associates with enhanced exocyst-mediated protein secretion.Aging Cell2022
34942634Evolution of enhanced innate immune evasion by SARS-CoV-2.Nature2022
35063084Tau interactome maps synaptic and mitochondrial processes associated with neurodegeneration.Cell2022
35332335Publisher Correction: Evolution of enhanced innate immune evasion by SARS-CoV-2.Nature2022
35266954The E3 ligase TRIM1 ubiquitinates LRRK2 and controls its localization, degradation, and toxicity.J Cell Biol2022
34031651CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.Res Sq2021
33854239The AMBRA1 E3 ligase adaptor regulates the stability of cyclin D.Nature2021
33729787CIDer: A Statistical Framework for Interpreting Differences in CID and HCD Fragmentation.J Proteome Res2021
33891876Chaperone-mediated autophagy prevents collapse of the neuronal metastable proteome.Cell2021
34591613Interpretation of cancer mutations using a multiscale map of protein systems.Science2021
34591612A protein interaction landscape of breast cancer.Science2021
34646016Systems-level effects of allosteric perturbations to a model molecular switch.Nature2021
34556855Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy.Nat Microbiol2021
34551310Brown adipocyte ATF4 activation improves thermoregulation and systemic metabolism.Cell Rep2021
34546978Caveolin-1 and Sox-2 are predictive biomarkers of cetuximab response in head and neck cancer.JCI Insight2021
34779417Therapeutic implications of activating noncanonical PIK3CA mutations in head and neck squamous cell carcinoma.J Clin Invest2021
34591642A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity.Science2021
34019840Adhesion-mediated mechanosignaling forces mitohormesis.Cell Metab2021
34127972Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant.bioRxiv2021
34013269CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.bioRxiv2021
34241634A ciliopathy complex builds distal appendages to initiate ciliogenesis.J Cell Biol2021
34319755Toward Comprehensive Plasma Proteomics by Orthogonal Protease Digestion.J Proteome Res2021
32531271Unbiased Proteomic Profiling Uncovers a Targetable GNAS/PKA/PP2A Axis in Small Cell Lung Cancer Stem Cells.Cancer Cell2020
32084337A Quantitative Genetic Interaction Map of HIV Infection.Mol Cell2020
31951200Dynamic post-translational modification profiling of <i>Mycobacterium tuberculosis</i>-infected primary macrophages.Elife2020
33060197Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.Science2020
33154106An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike.Science2020
32579556The kinase Isr1 negatively regulates hexosamine biosynthesis in S. cerevisiae.PLoS Genet2020
32817938An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation.bioRxiv2020
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Collaborators

Nevan J Krogan (CM4AI)
University of California San Francisco
Co-authored papers 53
Mehdi Bouhaddou
J. David Gladstone Institutes
Co-authored papers 15
Margaret Soucheray
J. David Gladstone Institutes
Co-authored papers 13
Alicia L Richards
University of Wisconsin-Madison
Co-authored papers 12
Andrea Fossati
J. David Gladstone Institutes
Co-authored papers 11
David Jimenez-Morales
J. David Gladstone Institutes
Co-authored papers 10
Pedro Beltrao
Institute of Molecular Systems Biology, ETH Zurich
Co-authored papers 10
Gwendolyn M Jang
Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes
Co-authored papers 10
Adolfo Garc??a-Sastre
Icahn School of Medicine at Mount Sinai
Co-authored papers 10
Kevan M Shokat
University of California San Francisco
Co-authored papers 9
Natalia Jura
Cardiovascular Research Institute, University of California San Francisco
Co-authored papers 9
Judit Vill??n
University of Washington
Co-authored papers 9
Kris M White
Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG)
Co-authored papers 9
Jyoti Batra
J. David Gladstone Institutes
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Trey Ideker (CM4AI)
University of California San Diego
Co-authored papers 8
Lorena Zuliani-Alvarez
J. David Gladstone Institutes
Co-authored papers 8
Adrian Pelin
University of Ottawa
Co-authored papers 8
Kliment A Verba
University of California, University of California San Francisco
Co-authored papers 8
Kirsten Obernier (CM4AI)
University of California San Francisco
Co-authored papers 8
Hannes Braberg
University of California San Francisco
Co-authored papers 7
Tanja Kortemme
University of California san francisco
Co-authored papers 7
Danish Memon
European Bioinformatics Institute
Co-authored papers 6
Joseph B Hiatt
Fred Hutchinson Cancer Center
Co-authored papers 6
James S Fraser
University of California san francisco
Co-authored papers 6
Sergei Pourmal
University of California san francisco
Co-authored papers 6
Raphael Trenker
Cardiovascular Research Institute, University of California San Francisco
Co-authored papers 6
Marco Vignuzzi
Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG)
Co-authored papers 6
Jeffrey R Johnson
Gladstone Institutes
Co-authored papers 6
David A Agard
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