
Associate Professor
P_Bioengineering
+1 415 734-2767
My interest is in using proteomics approaches to advance our understanding of both basic and disease biology. Of particular interest to me is the study of protein-protein interactions/complexes and post-translational modification signaling in the context of infection and neurodegeneration.
My lab at UCSF is encompassed within the larger lab of Nevan Krogan. This provides scientists the best of both worlds - access to big-lab support and resources, but with strong small-lab mentorship. Additionally, I manage the proteomics facility at both the UCSF Weill Institute for Neurosciences, and at the Gladstone Institutes, where I am a visiting scientist.
Publications
Anti-restriction functions of injected phage proteins revealed by peeling back layers of bacterial immunity.
Nature communications
Structure-based discovery of highly bioavailable, covalent, broad-spectrum coronavirus MPro inhibitors with potent in vivo efficacy.
Science advances
The Chlamydia effector Dre1 binds dynactin to reposition host organelles during infection.
Cell reports
Enhanced RNA replication and pathogenesis in recent SARS-CoV-2 variants harboring the L260F mutation in NSP6.
PLoS pathogens
Plasma proteomics for novel biomarker discovery in childhood tuberculosis.
medRxiv : the preprint server for health sciences
Lysosomal proteomics reveals mechanisms of neuronal apoE4associated lysosomal dysfunction.
bioRxiv : the preprint server for biology
Affinity Purification Mass Spectrometry on the Orbitrap-Astral Mass Spectrometer Enables High-Throughput Protein-Protein Interaction Mapping.
Journal of proteome research
Extracellular matrix proteolysis maintains synapse plasticity during brain development.
bioRxiv : the preprint server for biology
Coupled equilibria of dimerization and lipid binding modulate SARS Cov 2 Orf9b interactions and interferon response.
bioRxiv : the preprint server for biology
EGFR and EGFRvIII coopt host defense pathways, promoting progression in glioblastoma.
Neuro-Oncology
Malaria exposure remodels the plasma proteome of Ghanaian children.
BMC infectious diseases
BPS2025 - A matter of perspective: Integrative ensemble modeling of viral proteins.
Biophysical Journal
Tax1bp1 enhances bacterial virulence and promotes inflammatory responses during Mycobacterium tuberculosis infection of alveolar macrophages.
bioRxiv : the preprint server for biology
CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis.
bioRxiv : the preprint server for biology
Protocol for mapping differential protein-protein interaction networks using affinity purification-mass spectrometry.
STAR protocols
MerlinS13 phosphorylation regulates meningioma Wnt signaling and magnetic resonance imaging features.
Nature communications
The Mac1 ADP-ribosylhydrolase is a Therapeutic Target for SARS-CoV-2.
bioRxiv : the preprint server for biology
Multiscale photocatalytic proximity labeling reveals cell surface neighbors on and between cells.
Science (New York, N.Y.)
Characterization of a lipid-based jumbo phage compartment as a hub for early phage infection.
Cell host & microbe
The disease-causing tau V337M mutation induces tau hypophosphorylation and perturbs axon morphology pathways.
bioRxiv : the preprint server for biology
The Chlamydia trachomatis Inc Tri1 interacts with TRAF7 to displace native TRAF7 interacting partners.
Microbiology spectrum
ATG7(2) Interacts With Metabolic Proteins and Regulates Central Energy Metabolism.
Traffic (Copenhagen, Denmark)
Spatial control of sensory adaptation modulates mechanosensing in Pseudomonas aeruginosa.
bioRxiv : the preprint server for biology
The Chlamydia trachomatis Inc Tri1 interacts with TRAF7 to displace native TRAF7 interacting partners.
bioRxiv : the preprint server for biology
A foundational atlas of autism protein interactions reveals molecular convergence.
bioRxiv : the preprint server for biology
Epigenetic reprogramming shapes the cellular landscape of schwannoma.
Nature communications
Cross-family small GTPase ubiquitination by the intracellular pathogen Legionella pneumophila.
Molecular biology of the cell
In vivo protein turnover rates in varying oxygen tensions nominate MYBBP1A as a mediator of the hyperoxia response.
Science advances
Molecular determinants of the crosstalk between endosomal microautophagy and chaperone-mediated autophagy.
Cell reports
Multi-scale photocatalytic proximity labeling reveals cell surface neighbors on and between cells.
bioRxiv : the preprint server for biology
A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response.
Nature cell biology
High-throughput chemogenetic drug screening reveals PKC-RhoA/PKN as a targetable signaling vulnerability in GNAQ-driven uveal melanoma.
Cell reports. Medicine
Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets.
Nature communications
Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis.
Cell host & microbe
Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping.
Nature communications
Cross-family small GTPase ubiquitination by the intracellular pathogen Legionella pneumophila.
bioRxiv : the preprint server for biology
Functional analysis of a common BAG3 allele associated with protection from heart failure.
Nature Cardiovascular Research
Deep learning from harmonized peptide libraries enables retention time prediction of diverse post translational modifications.
bioRxiv : the preprint server for biology
Quantitative proteomic analysis reveals apoE4-dependent phosphorylation of the actin-regulating protein VASP.
Molecular & cellular proteomics : MCP
MerlinS13 phosphorylation controls meningioma Wnt signaling and magnetic resonance imaging features.
Research square
Next-generation interaction proteomics for quantitative Jumbophage-bacteria interaction mapping.
bioRxiv : the preprint server for biology
Oncogenic PKA signaling increases c-MYC protein expression through multiple targetable mechanisms.
eLife
Quantitative proteomic analysis reveals apoE4-dependent phosphorylation of the actin regulating protein VASP.
Alzheimer's & Dementia
Abstract B016: Inhibition of KRASG12C in colon cancer illustrates a link between beta-catenin, WNK, and the GID complex.
Cancer research
Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis.
bioRxiv : the preprint server for biology
CSIG-37. MERLIN S13 DEPHOSPHORYLATION DRIVES MENINGIOMA WNT SIGNALLING AND CELL PROLIFERATION.
Neuro-Oncology
EPCO-01. EPIGENETIC REPROGRAMMING SHAPES THE MOLECULAR AND CELLULAR LANDSCAPE OF SCHWANNOMA.
Neuro-Oncology
Resistance to ATR Inhibitors Is Mediated by Loss of the Nonsense-Mediated Decay Factor UPF2.
Cancer research
Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities.
Nature genetics
The E3 ligase TRIM1 ubiquitinates LRRK2 and controls its localization, degradation, and toxicity.
The Journal of cell biology
Data-Independent Acquisition Protease-Multiplexing Enables Increased Proteome Sequence Coverage Across Multiple Fragmentation Modes.
Journal of proteome research
Therapeutic implications of activating noncanonical PIK3CA mutations in head and neck squamous cell carcinoma.
The Journal of clinical investigation
Caveolin-1 and Sox-2 are predictive biomarkers of cetuximab response in head and neck cancer.
JCI insight
A protein interaction landscape of breast cancer.
Science (New York, N.Y.)
A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity.
Science (New York, N.Y.)
Interpretation of cancer mutations using a multiscale map of protein systems.
Science (New York, N.Y.)
Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy.
Nature microbiology
Toward Comprehensive Plasma Proteomics by Orthogonal Protease Digestion.
Journal of proteome research
A ciliopathy complex builds distal appendages to initiate ciliogenesis.
The Journal of cell biology
Adhesion-mediated mechanosignaling forces mitohormesis.
Cell metabolism
CIDer: A Statistical Framework for Interpreting Differences in CID and HCD Fragmentation.
Journal of proteome research
An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike.
Science (New York, N.Y.)
Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.
Science (New York, N.Y.)
Unbiased Proteomic Profiling Uncovers a Targetable GNAS/PKA/PP2A Axis in Small Cell Lung Cancer Stem Cells.
Cancer cell
A Quantitative Genetic Interaction Map of HIV Infection.
Molecular cell
Dynamic post-translational modification profiling of M. tuberculosis-infected primary macrophages.
eLife
The functional landscape of the human phosphoproteome.
Nature Biotechnology
Systematic Identification of Host Cell Regulators of Legionella pneumophila Pathogenesis Using a Genome-wide CRISPR Screen.
Cell host & microbe
KRASG12C inhibition produces a driver-limited state revealing collateral dependencies.
Science signaling
Neuronal Apolipoprotein E4 Expression Results in Proteome-Wide Alterations and Compromises Bioenergetic Capacity by Disrupting Mitochondrial Function.
Journal of Alzheimer's disease : JAD
TCO, a Putative Transcriptional Regulator in Arabidopsis, Is a Target of the Protein Kinase CK2.
International journal of molecular sciences
Multiple Routes to Oncogenesis are Promoted by the Human Papillomavirus-Host Protein Network.
Cancer discovery
Sympathetic inputs regulate adaptive thermogenesis in brown adipose tissue through cAMP-Salt inducible kinase axis.
Scientific reports
Proteome Imbalance of Mitochondrial Electron Transport Chain in Brown Adipocytes Leads to Metabolic Benefits.
Cell metabolism
Evolution of protein phosphorylation across 18 fungal species.
Science (New York, N.Y.)
Enrichment of Modified Peptides via Immunoaffinity Precipitation with Modification-Specific Antibodies.
Cold Spring Harbor protocols
Enrichment of Phosphopeptides via Immobilized Metal Affinity Chromatography.
Cold Spring Harbor protocols
Proteomic Analysis of Protein Posttranslational Modifications by Mass Spectrometry.
Cold Spring Harbor protocols
Phosphorylation of ubiquitin at Ser65 affects its polymerization, targets, and proteome-wide turnover.
EMBO reports
E2~Ub conjugates regulate the kinase activity of Shigella effector OspG during pathogenesis.
The EMBO journal
Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.
Nature methods
Affinity-based probes based on type II kinase inhibitors.
Journal of the American Chemical Society
Tra1 has specific regulatory roles, rather than global functions, within the SAGA co-activator complex.
The EMBO journal
Value of using multiple proteases for large-scale mass spectrometry-based proteomics.
Journal of proteome research
Phosphoproteomics for the masses.
ACS chemical biology
Large-scale phosphoprotein analysis in Medicago truncatula roots provides insight into in vivo kinase activity in legumes.
Plant physiology
Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures.
Analytical chemistry
A new probabilistic database search algorithm for ETD spectra.
Journal of proteome research
Toward defining the phosphoproteome of Xenopus laevis embryos.
Developmental dynamics : an official publication of the American Association of Anatomists
Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry.
Proceedings of the National Academy of Sciences of the United States of America
A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer.
Journal of proteome research
Tandem phosphorylation of Ser-911 and Thr-912 at the C terminus of yeast plasma membrane H+-ATPase leads to glucose-dependent activation.
The Journal of biological chemistry
Probing the dynamics of O-GlcNAc glycosylation in the brain using quantitative proteomics.
Nature chemical biology