
QBI Director and Professor
P_Bioengineering
+1 415 476-2980
My lab at UCSF focuses on developing and applying quantitative, systematic proteomic and genetic approaches to study complex biological and biomedical problems. At present time, my group is focused on studying cancer, infectious disease, including tuberculosis, and psychiatric disorders.
Krogen Lab: https://kroganlab.ucsf.edu/krogan-lab
Publications
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
Coupled equilibria of dimerization and lipid binding modulate SARS Cov 2 Orf9b interactions and interferon response.
bioRxiv : the preprint server for biology
MerlinS13 phosphorylation regulates meningioma Wnt signaling and magnetic resonance imaging features.
Frontiers in medicine
Fate of telomere entanglements is dictated by the timing of anaphase midregion nuclear envelope breakdown.
Frontiers in medicine
An automated proximity proteomics pipeline for subcellular proteome and protein interaction mapping.
Epigenetic reprogramming shapes the cellular landscape of schwannoma.
Frontiers in medicine
Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets.
Frontiers in medicine
Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping.
Frontiers in medicine
Structural insights into regulation of the PEAK3 pseudokinase scaffold by 14-3-3.
Frontiers in medicine
Dengue virus NS5 degrades ERC1 during infection to antagonize NF-kB activation.
Journal of immigrant and minority health
MerlinS13 phosphorylation controls meningioma Wnt signaling and magnetic resonance imaging features.
Oncogenic PKA signaling increases c-MYC protein expression through multiple targetable mechanisms.
AIDS (London, England)
Structure-function analysis of enterovirus protease 2A in complex with its essential host factor SETD3.
Frontiers in medicine
A functional map of HIV-host interactions in primary human T cells.
Frontiers in medicine
Leveraging modeling and simulation to optimize the therapeutic window for epigenetic modifier drugs.
Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission.
Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy.
JAMA
Chemical-genetic interrogation of RNA polymerase mutants reveals structure-function relationships and physiological tradeoffs.
Journal of the International Association of Providers of AIDS Care
SUMO is a pervasive regulator of meiosis.
AIDS (London, England)
SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling.
Journal of immigrant and minority health
Functional genomic screens identify human host factors for SARS-CoV-2 and common cold coronaviruses.
mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1.
Frontiers in medicine
A Quantitative Genetic Interaction Map of HIV Infection.
Journal of the International Association of Providers of AIDS Care
Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages.
AIDS (London, England)
PEAK3/C19orf35 pseudokinase, a new NFK3 kinase family member, inhibits CrkII through dimerization.
Journal of immigrant and minority health
Chaperone-mediated reflux of secretory proteins to the cytosol during endoplasmic reticulum stress.
Journal of immigrant and minority health
Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins.
Journal of the International Association of Providers of AIDS Care
Genetic analysis reveals functions of atypical polyubiquitin chains.
AIDS (London, England)
The Cellular NMD Pathway Restricts Zika Virus Infection and Is Targeted by the Viral Capsid Protein.
EpCAM homo-oligomerization is not the basis for its role in cell-cell adhesion.
The Lancet. Microbe
Mycobacterial Mutagenesis and Drug Resistance Are Controlled by Phosphorylation- and Cardiolipin-Mediated Inhibition of the RecA Coprotease.
Journal of the International Association of Providers of AIDS Care
An Mtb-Human Protein-Protein Interaction Map Identifies a Switch between Host Antiviral and Antibacterial Responses.
Journal of the International Association of Providers of AIDS Care
Sympathetic inputs regulate adaptive thermogenesis in brown adipose tissue through cAMP-Salt inducible kinase axis.
The Lancet. Microbe
The HIV-1 Tat protein recruits a ubiquitin ligase to reorganize the 7SK snRNP for transcriptional activation.
AIDS (London, England)
Author Correction: SMARCA2-regulated host cell factors are required for MxA restriction of influenza A viruses.
The Lancet. Microbe
The H3K36me2 Methyltransferase Nsd1 Demarcates PRC2-Mediated H3K27me2 and H3K27me3 Domains in Embryonic Stem Cells.
Journal of the International Association of Providers of AIDS Care
SMARCA2-regulated host cell factors are required for MxA restriction of influenza A viruses.
The Lancet. Microbe
Metabolic reprogramming of human CD8+ memory T cells through loss of SIRT1.
Clinical gerontologist
Mutations in the X-linked ATP6AP2 cause a glycosylation disorder with autophagic defects.
Clinical gerontologist
The Tyrosine Kinase Inhibitor Gefitinib Restricts Mycobacterium tuberculosis Growth through Increased Lysosomal Biogenesis and Modulation of Cytokine Signaling.
AIDS and behavior
PJA2 ubiquitinates the HIV-1 Tat protein with atypical chain linkages to activate viral transcription.
The Lancet. Microbe
Chlamydia interfere with an interaction between the mannose-6-phosphate receptor and sorting nexins to counteract host restriction.
AIDS (London, England)
Suppression of C9orf72 RNA repeat-induced neurotoxicity by the ALS-associated RNA-binding protein Zfp106.
AIDS (London, England)
Non-degradative Ubiquitination of Protein Kinases.
Current opinion in cell biology
Targeting Viral Proteostasis Limits Influenza Virus, HIV, and Dengue Virus Infection.
Journal of cell science
Meta- and Orthogonal Integration of Influenza "OMICs" Data Defines a Role for UBR4 in Virus Budding.
Discovery and functional characterization of a neomorphic PTEN mutation.
Journal of immigrant and minority health
Critical role of acetylation in tau-mediated neurodegeneration and cognitive deficits.
P_Pharmaceutical Chemistry
Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes.
Current opinion in cell biology
Centriolar satellites assemble centrosomal microcephaly proteins to recruit CDK2 and promote centriole duplication.
AIDS (London, England)
The cancer cell map initiative: defining the hallmark networks of cancer.
Journal of the International Association of Providers of AIDS Care
Pharmacological dimerization and activation of the exchange factor eIF2B antagonizes the integrated stress response.
AIDS (London, England)
A combined proteomics/genomics approach links hepatitis C virus infection with nonsense-mediated mRNA decay.
Journal of the International Association of Providers of AIDS Care
Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes.
Journal of the International Association of Providers of AIDS Care
AFF1 is a ubiquitous P-TEFb partner to enable Tat extraction of P-TEFb from 7SK snRNP and formation of SECs for HIV transactivation.
Journal of immigrant and minority health
A lipid E-MAP identifies Ubx2 as a critical regulator of lipid saturation and lipid bilayer stress.
Journal of the International Association of Providers of AIDS Care
Bringing it all together: big data and HIV research.
The Lancet regional health. Southeast Asia
The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat.
AIDS (London, England)
From systems to structure: bridging networks and mechanism.
Journal of the International Association of Providers of AIDS Care
CBFß stabilizes HIV Vif to counteract APOBEC3 at the expense of RUNX1 target gene expression.
Journal of the International Association of Providers of AIDS Care
Dissection of DNA damage responses using multiconditional genetic interaction maps.
Journal of the International Association of Providers of AIDS Care
HIV-1 Tat recruits transcription elongation factors dispersed along a flexible AFF4 scaffold.
Journal of immigrant and minority health
Hierarchical modularity and the evolution of genetic interactomes across species.
Journal of the International Association of Providers of AIDS Care
Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress.
Journal of immigrant and minority health
Yeast SREBP cleavage activation requires the Golgi Dsc E3 ligase complex.
Journal of the International Association of Providers of AIDS Care
HIV-1 Tat and host AFF4 recruit two transcription elongation factors into a bifunctional complex for coordinated activation of HIV-1 transcription.
Journal of the International Association of Providers of AIDS Care
A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300.
A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing.
Journal of the International Association of Providers of AIDS Care
A single SR-like protein, Npl3, promotes pre-mRNA splicing in budding yeast.
Journal of the International Association of Providers of AIDS Care
Functional maps of protein complexes from quantitative genetic interaction data.
Current opinion in cell biology
H2B ubiquitylation acts as a barrier to Ctk1 nucleosomal recruitment prior to removal by Ubp8 within a SAGA-related complex.
Journal of the International Association of Providers of AIDS Care
CCR4/NOT complex associates with the proteasome and regulates histone methylation.
Journal of immigrant and minority health
Maintenance of low histone ubiquitylation by Ubp10 correlates with telomere-proximal Sir2 association and gene silencing.
Journal of the International Association of Providers of AIDS Care
Proteasome involvement in the repair of DNA double-strand breaks.
Journal of the International Association of Providers of AIDS Care
Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4.
Journal of immigrant and minority health
High-definition macromolecular composition of yeast RNA-processing complexes.
Journal of the International Association of Providers of AIDS Care
A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1.
Journal of the International Association of Providers of AIDS Care
The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation.
Journal of the International Association of Providers of AIDS Care
Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter.
Journal of the International Association of Providers of AIDS Care
COMPASS: a complex of proteins associated with a trithorax-related SET domain protein.
Journal of immigrant and minority health