Nevan J. Krogan

The paper introduces the CM4AI project, which aims to create AI-ready datasets of human cell architecture using multimodal data from cell lines.

This study identifies CebN, a Chlamydia trachomatis effector that targets nucleoporins and Rae1 to disrupt STAT1 nuclear import, aiding bacterial survival.

The paper identifies nuclear envelope homeostasis as critical for resolving telomere entanglements in fission yeast through genetic screens and functional analysis.

The paper identifies novel protein and RNA interactions of APOBEC3 enzymes, revealing deamination-independent roles in RNA biology and cancer.

This study shows ORF8 suppresses viral particle production by interacting with Spike and causing Golgi fragmentation, supporting evolutionary pressure to delete ORF8 in SARS-CoV-2 variants.

This study identifies a spatial mechanism of sensory adaptation in Pseudomonas aeruginosa, revealing how enzyme localization modulates mechanosensing and virulence.

This study identifies how Legionella pneumophila modifies host ubiquitination during infection, revealing widespread monoubiquitination of small GTPases and the role of SidC/SdcA effectors.

The paper constructs a PPI network of 100 high-confidence ASD genes, identifies novel interactions, and uses AlphaFold-Multimer to prioritize variants for functional validation in organoids.

This study investigates the functional impact of a BAG3 allele associated with reduced heart failure risk, showing it enhances cardiomyocyte stress resistance through altered protein interactions.

The paper identifies the Mediator Kinase Module's role in DNA damage response and transcriptional regulation across species.

This study uses co-fractionation mass spectrometry to map host-pathogen and pathogen-pathogen interactions in jumbophages infecting Pseudomonas aeruginosa, revealing over 6000 interactions and novel viral components.

The paper systematically analyzes proteomic and genomic data of SARS-CoV-2 variants to identify how mutations affect viral gene expression, host interactions, and immune evasion.

The paper identifies reduced EXOSC2 expression as protective against SARS-CoV-2 infection and clinical COVID-19 by inhibiting viral replication and upregulating antiviral genes.

The paper shows that BET proteins are antiviral factors against SARS-CoV-2, and the viral E protein neutralizes BET-mediated post-entry antiviral effects.

The paper shows apoE4 increases VASP phosphorylation, disrupting actin interactions and affecting neurite outgrowth in Neuro-2a cells.

The paper identifies novel regulators of mu opioid receptor signaling and trafficking using proximity labeling and proteomics.

The paper maps Tau interactomes in neurons using APEX and AP-MS to reveal activity-dependent interactions and FTD mutation effects on mitochondrial associations in neurodegenerative diseases.

This study identifies TRIM1 as an E3 ligase that ubiquitinates LRRK2, regulating its localization, degradation, and toxicity in Parkinson's Disease.

The paper investigates how the GTPase Ran/Gsp1 achieves functional multi-specificity through biophysical and genetic perturbations, revealing that its effects are linked to kinetic parameters of the switch cycle rather than direct interaction sites.

This paper describes a method to efficiently generate genetically modified primary human myeloid cells using CRISPR-Cas9 RNP nucleofection, demonstrating its utility in studying HIV-1 infection and myeloid cell biology.

The paper uses chemical-genetic analysis of RNA polymerase mutants to uncover structure-function relationships and physiological trade-offs in Escherichia coli.

The 73-amino-acid SARS-CoV-2 membrane-associated protein ORF9c suppresses interferon, antigen presentation, and complement pathways while inducing IL-6 signaling in lung epithelial cells, an effect blunted by proteasome or VCP inhibition.

This paper identifies Isr1 as a negative regulator of the hexosamine biosynthesis pathway in yeast, showing it inhibits Gfa1 and modulates UDP-GlcNAc synthesis in response to cell cycle and nutrient signals.

The paper creates a comprehensive human phosphoproteome by integrating 6,801 phospho-enriched mass spectrometry experiments and prioritizes functional phosphosites using machine learning.

The paper identifies 2747 SUMO modification sites in budding yeast meiosis, revealing SUMO's role in chromosome organization and recombination.

The paper investigates how acetylation and phosphorylation of RNA polymerase II CTD interact through RPRD proteins, showing acetylation regulates phosphorylation and vice versa.

This study identifies ANKLE2 as a Zika virus target that regulates neuroblast asymmetric division, linking it to microcephaly and motor neuron disease through interactions with VRK1 and LLGL1.

The paper identifies NOSEMPE in brown adipocytes as a cause of mitochondrial ETC imbalance and shows it drives nonmitochondrial thermogenesis and metabolic improvement via ATF4 activation.

The paper uses proteomic analysis to identify TAX1BP1 as a mediator of autophagy targeting M. tuberculosis during macrophage infection.