
QBI Director and Professor
P_Bioengineering
+1 415 476-2980
Custom People Group
Dr. Krogan was born and raised in Regina, Saskatchewan, Canada, obtained his undergraduate degree from the University of Regina and his PhD from the University of Toronto. Dr. Krogan’s lab at UCSF focuses on developing and applying quantitative, systematic proteomic and genetic approaches to study complex biological and biomedical problems. At present time, the Krogan group is focused on studying cancer, infectious disease and psychiatric disorders.
Publications
Redefining druggable targets with artificial intelligence.
Nature biotechnology
Coronavirus protein interaction mapping in bat and human cells identifies molecular and genetic switches for immune evasion and replication.
bioRxiv : the preprint server for biology
Ebola virus VP35 NNLNS motif modulates viral RNA synthesis and MIB2-mediated signaling.
bioRxiv : the preprint server for biology
Programmable translational inhibition by a molecular glue-oligonucleotide conjugate.
bioRxiv : the preprint server for biology
A transcriptomic, proteomic, and functional genetic atlas dissects neurofibromin function in the peripheral nervous system.
Proceedings of the National Academy of Sciences of the United States of America
Inference of differential kinase interaction networks with KINference.
Bioinformatics (Oxford, England)
Paracrine Signals from HIV-1 Infected Immune Cells Reprogram Cervical Cancer Pathways.
bioRxiv : the preprint server for biology
AlphaFold models of host-pathogen interactions elucidate the prevalence and structural modes of molecular mimicry.
bioRxiv : the preprint server for biology
The Mediator Kinase Module regulates cell cycle re-entry and transcriptional responses following DNA damage.
bioRxiv : the preprint server for biology
Selective RNA sequestration in biomolecular condensates directs cell fate transitions.
bioRxiv : the preprint server for biology
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
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
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
Tax1bp1 enhances bacterial virulence and promotes inflammatory responses during Mycobacterium tuberculosis infection of alveolar macrophages.
bioRxiv : the preprint server for biology
A Perturbation Cell Atlas of Human Induced Pluripotent Stem Cells.
bioRxiv : the preprint server for biology
Protocol for mapping differential protein-protein interaction networks using affinity purification-mass spectrometry.
STAR protocols
Institutional Conversion to Energy-Efficient Ultra-Low Freezers Decreases Carbon Footprint and Reduces Energy Costs.
Biopreservation and biobanking
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
Parallel genetic screens identify nuclear envelope homeostasis as a key determinant of telomere entanglement resolution in fission yeast.
G3 (Bethesda, Md.)
A proximity proteomics pipeline with improved reproducibility and throughput.
Molecular systems biology
Fate of telomere entanglements is dictated by the timing of anaphase midregion nuclear envelope breakdown.
Nature communications
The Chlamydia trachomatis Inc Tri1 interacts with TRAF7 to displace native TRAF7 interacting partners.
Microbiology spectrum
Predicted mechanistic impacts of human protein missense variants.
bioRxiv : the preprint server for biology
Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines.
bioRxiv : the preprint server for biology
A proximity proteomics pipeline with improved reproducibility and throughput.
bioRxiv : the preprint server for biology
Global mapping of the Chlamydia trachomatis conventional secreted effector - host interactome reveals CebN interacts with nucleoporins and Rae1 to impede STAT1 nuclear translocation.
bioRxiv : the preprint server for biology
ATG7(2) Interacts With Metabolic Proteins and Regulates Central Energy Metabolism.
Traffic (Copenhagen, Denmark)
Protein Interaction Map of APOBEC3 Enzyme Family Reveals Deamination-Independent Role in Cellular Function.
Molecular & cellular proteomics : MCP
Profiling the proximal proteome of the activated μ-opioid receptor.
Nature chemical biology
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
Protein interaction map of APOBEC3 enzyme family reveals deamination-independent role in cellular function.
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
Molecular determinants of the crosstalk between endosomal microautophagy and chaperone-mediated autophagy.
Cell reports
A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response.
Nature cell biology
The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5.
Stem cell reports
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
A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication in vivo.
PLoS pathogens
Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping.
Nature communications
Network modeling suggests HIV infection phenocopies PI3K-AKT pathway mutations to enhance HPV-associated cervical cancer.
Molecular omics
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
Structural insights into regulation of the PEAK3 pseudokinase scaffold by 14-3-3.
Nature communications
Lessons learned for pandemic preparedness: A collaborative network is imperative.
Cell host & microbe
Defining blood-induced microglia functions in neurodegeneration through multiomic profiling.
Nature immunology
Dengue virus NS5 degrades ERC1 during infection to antagonize NF-kB activation.
Proceedings of the National Academy of Sciences of the United States of America
A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis in vivo.
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
Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13.
Nature structural & molecular biology
Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13.
bioRxiv : the preprint server for biology
Oncogenic PKA signaling increases c-MYC protein expression through multiple targetable mechanisms.
eLife
Workshop-based learning and networking: a scalable model for research capacity strengthening in low- and middle-income countries.
Global health action
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
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
Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication.
Life science alliance
Structure-function analysis of enterovirus protease 2A in complex with its essential host factor SETD3.
Nature communications
Correction: Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer.
Cancer research
Editor's Note: Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer.
Cancer research
A Whole-Genome CRISPR Screen Identifies AHR Loss as a Mechanism of Resistance to a PARP7 Inhibitor.
Molecular cancer therapeutics
DLX1 and the NuRD complex cooperate in enhancer decommissioning and transcriptional repression.
Development (Cambridge, England)
Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities.
Nature genetics
Integrative structure determination of histones H3 and H4 using genetic interactions.
The FEBS journal
A functional map of HIV-host interactions in primary human T cells.
Nature communications
The E3 ligase TRIM1 ubiquitinates LRRK2 and controls its localization, degradation, and toxicity.
The Journal of cell biology
The RNA helicase DHX16 recognizes specific viral RNA to trigger RIG-I-dependent innate antiviral immunity.
Cell reports
Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication.
bioRxiv : the preprint server for biology
Leveraging modeling and simulation to optimize the therapeutic window for epigenetic modifier drugs.
Pharmacology & therapeutics
Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission.
Cell host & microbe
From systems to structure - using genetic data to model protein structures.
Nature reviews. Genetics
Preclinical and randomized phase I studies of plitidepsin in adults hospitalized with COVID-19.
Life science alliance
Comparative Analysis of T-Cell Spatial Proteomics and the Influence of HIV Expression.
Molecular & cellular proteomics : MCP
SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein.
bioRxiv : the preprint server for biology
Therapeutic implications of activating noncanonical PIK3CA mutations in head and neck squamous cell carcinoma.
The Journal of clinical investigation
Viral E Protein Neutralizes BET Protein-Mediated Post-Entry Antagonism of SARS-CoV-2.
bioRxiv : the preprint server for biology
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
Target Discovery for Host-Directed Antiviral Therapies: Application of Proteomics Approaches.
mSystems
An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia.
Current biology : CB
Characterization of an A3G-VifHIV-1-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host-Pathogen Complexes.
Molecular & cellular proteomics : MCP
Non-canonical proline-tyrosine interactions with multiple host proteins regulate Ebola virus infection.
The EMBO journal
A ciliopathy complex builds distal appendages to initiate ciliogenesis.
The Journal of cell biology
An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia.
Current biology : CB
Drug-induced phospholipidosis confounds drug repurposing for SARS-CoV-2.
Science (New York, N.Y.)
Endosomal cAMP production broadly impacts the cellular phosphoproteome.
The Journal of biological chemistry
Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant.
bioRxiv : the preprint server for biology
Plitidepsin has a positive therapeutic index in adult patients with COVID-19 requiring hospitalization.
medRxiv : the preprint server for health sciences
Adhesion-mediated mechanosignaling forces mitohormesis.
Cell metabolism
Chemical-genetic interrogation of RNA polymerase mutants reveals structure-function relationships and physiological tradeoffs.
Molecular cell
CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.
Research square
CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.
bioRxiv : the preprint server for biology
Efficient generation of isogenic primary human myeloid cells using CRISPR-Cas9 ribonucleoproteins.
Cell reports
Smoothened transduces Hedgehog signals via activity-dependent sequestration of PKA catalytic subunits.
PLoS biology
Phospholipidosis is a shared mechanism underlying the in vitro antiviral activity of many repurposed drugs against SARS-CoV-2.
bioRxiv : the preprint server for biology
Host-directed therapies against early-lineage SARS-CoV-2 retain efficacy against B.1.1.7 variant.
bioRxiv : the preprint server for biology
Evaluating a New Class of AKT/mTOR Activators for HIV Latency Reversing Activity Ex Vivo and In Vivo.
Journal of virology
Plitidepsin has potent preclinical efficacy against SARS-CoV-2 by targeting the host protein eEF1A.
Science (New York, N.Y.)
Proteomic Approaches to Study SARS-CoV-2 Biology and COVID-19 Pathology.
Journal of proteome research
Mass spectrometry-based protein-protein interaction networks for the study of human diseases.
Molecular systems biology
Genetic interaction mapping informs integrative structure determination of protein complexes.
Science (New York, N.Y.)
An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike.
Science (New York, N.Y.)
SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling.
Proceedings of the National Academy of Sciences of the United States of America
Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.
Science (New York, N.Y.)
Functional genomic screens identify human host factors for SARS-CoV-2 and common cold coronaviruses.
bioRxiv : the preprint server for biology
Evaluation of SARS-CoV-2 serology assays reveals a range of test performance.
Nature biotechnology
SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells.
bioRxiv : the preprint server for biology
An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation.
bioRxiv : the preprint server for biology
Structural basis of CD4 downregulation by HIV-1 Nef.
Nature structural & molecular biology
Correction: Thioredoxin-related protein 32 is an arsenite-regulated thiol reductase of the proteasome 19 S particle.
The Journal of biological chemistry
Unbiased Proteomic Profiling Uncovers a Targetable GNAS/PKA/PP2A Axis in Small Cell Lung Cancer Stem Cells.
Cancer cell
The Landscape of Human Cancer Proteins Targeted by SARS-CoV-2.
Cancer discovery
Test performance evaluation of SARS-CoV-2 serological assays.
medRxiv : the preprint server for health sciences
mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1.
Nature communications
A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing.
bioRxiv : the preprint server for biology
Cyclophilin A Prevents HIV-1 Restriction in Lymphocytes by Blocking Human TRIM5α Binding to the Viral Core.
Cell reports
A Quantitative Genetic Interaction Map of HIV Infection.
Molecular cell
A systems approach to infectious disease.
Nature reviews. Genetics
The functional landscape of the human phosphoproteome.
Nature biotechnology
Mutations in ANKLE2, a ZIKA Virus Target, Disrupt an Asymmetric Cell Division Pathway in Drosophila Neuroblasts to Cause Microcephaly.
Developmental cell
Systematic Identification of Host Cell Regulators of Legionella pneumophila Pathogenesis Using a Genome-wide CRISPR Screen.
Cell host & microbe
Enterovirus pathogenesis requires the host methyltransferase SETD3.
Nature microbiology
Regulation of Skn7-dependent, oxidative stress-induced genes by the RNA polymerase II-CTD phosphatase, Fcp1, and Mediator kinase subunit, Cdk8, in yeast.
The Journal of biological chemistry
Synthetic Essentiality of Metabolic Regulator PDHK1 in PTEN-Deficient Cells and Cancers.
Cell reports
Large dataset enables prediction of repair after CRISPR-Cas9 editing in primary T cells.
Nature biotechnology
PEAK3/C19orf35 pseudokinase, a new NFK3 kinase family member, inhibits CrkII through dimerization.
Proceedings of the National Academy of Sciences of the United States of America
Mapping the protein-protein and genetic interactions of cancer to guide precision medicine.
Current opinion in genetics & development
Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis.
Development (Cambridge, England)
ARIH2 Is a Vif-Dependent Regulator of CUL5-Mediated APOBEC3G Degradation in HIV Infection.
Cell host & microbe
Heart failure drug proscillaridin A targets MYC overexpressing leukemia through global loss of lysine acetylation.
Journal of experimental & clinical cancer research : CR
Chaperone-mediated reflux of secretory proteins to the cytosol during endoplasmic reticulum stress.
Proceedings of the National Academy of Sciences of the United States of America
Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins.
Molecular cell
SIRT3 controls brown fat thermogenesis by deacetylation regulation of pathways upstream of UCP1.
Molecular metabolism
Identification of antiviral roles for the exon-junction complex and nonsense-mediated decay in flaviviral infection.
Nature microbiology
CRISPR-Cas9 genome engineering of primary CD4+ T cells for the interrogation of HIV-host factor interactions.
Nature protocols
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
Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication.
Cell
Virus and host interactions critical for filoviral RNA synthesis as therapeutic targets.
Antiviral research
The Cellular NMD Pathway Restricts Zika Virus Infection and Is Targeted by the Viral Capsid Protein.
mBio
Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus-Host Protein Network.
Cancer discovery
Influenza virus infection causes global RNAPII termination defects.
Nature structural & molecular biology
CRL4AMBRA1 targets Elongin C for ubiquitination and degradation to modulate CRL5 signaling.
The EMBO journal
An Mtb-Human Protein-Protein Interaction Map Identifies a Switch between Host Antiviral and Antibacterial Responses.
Molecular cell
Sympathetic inputs regulate adaptive thermogenesis in brown adipose tissue through cAMP-Salt inducible kinase axis.
Scientific reports
Author Correction: SMARCA2-regulated host cell factors are required for MxA restriction of influenza A viruses.
Scientific reports
The H3K36me2 Methyltransferase Nsd1 Demarcates PRC2-Mediated H3K27me2 and H3K27me3 Domains in Embryonic Stem Cells.
Molecular cell
SIRT1 Deacetylates Tau and Reduces Pathogenic Tau Spread in a Mouse Model of Tauopathy.
The Journal of neuroscience : the official journal of the Society for Neuroscience
Proteome Imbalance of Mitochondrial Electron Transport Chain in Brown Adipocytes Leads to Metabolic Benefits.
Cell metabolism
How many human proteoforms are there?
Nature chemical biology
Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer.
Cancer research
Genetic Interaction Mapping in Schizosaccharomyces pombe Using the Pombe Epistasis Mapper (PEM) System and a ROTOR HDA Colony Replicating Robot in a 1536 Array Format.
Cold Spring Harbor protocols
Genetic Interaction Score (S-Score) Calculation, Clustering, and Visualization of Genetic Interaction Profiles for Yeast.
Cold Spring Harbor protocols
High-Throughput Quantitative Genetic Interaction Mapping in the Fission Yeast Schizosaccharomyces pombe.
Cold Spring Harbor protocols
SMARCA2-regulated host cell factors are required for MxA restriction of influenza A viruses.
Scientific reports
Fab-based inhibitors reveal ubiquitin independent functions for HIV Vif neutralization of APOBEC3 restriction factors.
PLoS pathogens
DNA Preparation from Schizosaccharomyces pombe.
Cold Spring Harbor protocols
Transformation of Schizosaccharomyces pombe in a 96-Well Format.
Cold Spring Harbor protocols
Evolutionary Proteomics Uncovers Ancient Associations of Cilia with Signaling Pathways.
Developmental cell
Metabolic reprogramming of human CD8+ memory T cells through loss of SIRT1.
The Journal of experimental medicine
Mutations in the X-linked ATP6AP2 cause a glycosylation disorder with autophagic defects.
The Journal of experimental medicine
The Host E3-Ubiquitin Ligase TRIM6 Ubiquitinates the Ebola Virus VP35 Protein and Promotes Virus Replication.
Journal of virology
Virus-Like Vesicles of Kaposi's Sarcoma-Associated Herpesvirus Activate Lytic Replication by Triggering Differentiation Signaling.
Journal of virology
The Tyrosine Kinase Inhibitor Gefitinib Restricts Mycobacterium tuberculosis Growth through Increased Lysosomal Biogenesis and Modulation of Cytokine Signaling.
ACS infectious diseases
SMYD2-Mediated Histone Methylation Contributes to HIV-1 Latency.
Cell host & microbe
The histone variant H2A.Z promotes splicing of weak introns.
Genes & development
PJA2 ubiquitinates the HIV-1 Tat protein with atypical chain linkages to activate viral transcription.
Scientific reports
Systems-based analysis of RIG-I-dependent signalling identifies KHSRP as an inhibitor of RIG-I receptor activation.
Nature microbiology
A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors.
Nature genetics
The mTOR Complex Controls HIV Latency.
Cell host & microbe
G Protein-Coupled Receptor Endocytosis Confers Uniformity in Responses to Chemically Distinct Ligands.
Molecular pharmacology
A Herpesvirus Protein Selectively Inhibits Cellular mRNA Nuclear Export.
Cell host & microbe
Combined Action of Histone Reader Modules Regulates NuA4 Local Acetyltransferase Function but Not Its Recruitment on the Genome.
Molecular and cellular biology
A Cas9 Ribonucleoprotein Platform for Functional Genetic Studies of HIV-Host Interactions in Primary Human T Cells.
Cell reports
The Dengue Virus NS5 Protein Intrudes in the Cellular Spliceosome and Modulates Splicing.
PLoS pathogens
A Chemical-Genomic Screen of Neglected Antibiotics Reveals Illicit Transport of Kasugamycin and Blasticidin S.
PLoS genetics
Non-degradative Ubiquitination of Protein Kinases.
PLoS computational biology
A scaffold protein connects type IV pili with the Chp chemosensory system to mediate activation of virulence signaling in Pseudomonas aeruginosa.
Molecular microbiology
Nonsense-mediated decay regulates key components of homologous recombination.
Nucleic acids research
CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs.
Cell stem cell
Meta- and Orthogonal Integration of Influenza "OMICs" Data Defines a Role for UBR4 in Virus Budding.
Cell host & microbe
CDK11 in TREX/THOC Regulates HIV mRNA 3' End Processing.
Cell host & microbe
Discovery and functional characterization of a neomorphic PTEN mutation.
Proceedings of the National Academy of Sciences of the United States of America
Critical role of acetylation in tau-mediated neurodegeneration and cognitive deficits.
Nature medicine
Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes.
PLoS computational biology
Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells.
Cell systems
Comparative mapping of host-pathogen protein-protein interactions.
Current opinion in microbiology
Global Mapping of the Inc-Human Interactome Reveals that Retromer Restricts Chlamydia Infection.
Cell host & microbe
Spindle Checkpoint Factors Bub1 and Bub2 Promote DNA Double-Strand Break Repair by Nonhomologous End Joining.
Molecular and cellular biology
Differential genetic interactions of yeast stress response MAPK pathways.
Molecular systems biology
Genetic interaction mapping reveals a role for the SWI/SNF nucleosome remodeler in spliceosome activation in fission yeast.
PLoS genetics
Genetic Interaction Landscape Reveals Critical Requirements for Schizosaccharomyces pombe Brc1 in DNA Damage Response Mutants.
G3 (Bethesda, Md.)
Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST.
Current protocols in bioinformatics
A combined proteomics/genomics approach links hepatitis C virus infection with nonsense-mediated mRNA decay.
Molecular cell
Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes.
Molecular cell
Linking tumor mutations to drug responses via a quantitative chemical-genetic interaction map.
Cancer discovery
Regulation of Sufu activity by p66β and Mycbp provides new insight into vertebrate Hedgehog signaling.
Genes & development
Cyclin-dependent kinase 12 increases 3' end processing of growth factor-induced c-FOS transcripts.
Molecular and cellular biology
Acetylome profiling reveals overlap in the regulation of diverse processes by sirtuins, gcn5, and esa1.
Molecular & cellular proteomics : MCP
Quantitative analysis of triple-mutant genetic interactions.
Nature protocols
Yeast X-chromosome-associated protein 5 (Xap5) functions with H2A.Z to suppress aberrant transcripts.
EMBO reports
Genetic interaction analysis of point mutations enables interrogation of gene function at a residue-level resolution: exploring the applications of high-resolution genetic interaction mapping of point mutations.
BioEssays : news and reviews in molecular, cellular and developmental biology
Adventures in time and space: splicing efficiency and RNA polymerase II elongation rate.
RNA biology
Conditional genetic interactions of RTT107, SLX4, and HRQ1 reveal dynamic networks upon DNA damage in S. cerevisiae.
G3 (Bethesda, Md.)
A chaperone-assisted degradation pathway targets kinetochore proteins to ensure genome stability.
PLoS genetics
A Pil1-Sle1-Syj1-Tax4 functional pathway links eisosomes with PI(4,5)P2 regulation.
Journal of cell science
AFF1 is a ubiquitous P-TEFb partner to enable Tat extraction of P-TEFb from 7SK snRNP and formation of SECs for HIV transactivation.
Proceedings of the National Academy of Sciences of the United States of America
Evolution and functional cross-talk of protein post-translational modifications.
Molecular systems biology
IFI16 DNA sensor is required for death of lymphoid CD4 T cells abortively infected with HIV.
Science (New York, N.Y.)
High-resolution network biology: connecting sequence with function.
Nature reviews. Genetics
High-throughput genetic and gene expression analysis of the RNAPII-CTD reveals unexpected connections to SRB10/CDK8.
PLoS genetics
From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II.
Cell
A lipid E-MAP identifies Ubx2 as a critical regulator of lipid saturation and lipid bilayer stress.
Molecular cell
Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.
Nature methods
Bringing it all together: big data and HIV research.
AIDS (London, England)
Quantitative genetic-interaction mapping in mammalian cells.
Nature methods
From systems to structure: bridging networks and mechanism.
Molecular cell
CBFβ stabilizes HIV Vif to counteract APOBEC3 at the expense of RUNX1 target gene expression.
Molecular cell
Dispersed sites of HIV Vif-dependent polyubiquitination in the DNA deaminase APOBEC3F.
Journal of molecular biology
A gene ontology inferred from molecular networks.
Nature biotechnology
All or nothing: protein complexes flip essentiality between distantly related eukaryotes.
Genome biology and evolution
HIV-1 Tat recruits transcription elongation factors dispersed along a flexible AFF4 scaffold.
Proceedings of the National Academy of Sciences of the United States of America
Inhibition of RNA lariat debranching enzyme suppresses TDP-43 toxicity in ALS disease models.
Nature genetics
Replication fork collapse and genome instability in a deoxycytidylate deaminase mutant.
Molecular and cellular biology
Moloney leukemia virus type 10 inhibits reverse transcription and retrotransposition of intracisternal a particles.
Journal of virology
Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal.
PLoS genetics
Differential network biology.
Molecular systems biology
First-in-class small molecule inhibitors of the single-strand DNA cytosine deaminase APOBEC3G.
ACS chemical biology
Comparative interaction networks: bridging genotype to phenotype.
Advances in experimental medicine and biology
Host cell interactome of HIV-1 Rev includes RNA helicases involved in multiple facets of virus production.
Molecular & cellular proteomics : MCP
RNA polymerase II carboxyl-terminal domain phosphorylation regulates protein stability of the Set2 methyltransferase and histone H3 di- and trimethylation at lysine 36.
The Journal of biological chemistry
Eisosome proteins assemble into a membrane scaffold.
The Journal of cell biology
Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs.
BMC systems biology
Key functional regions in the histone variant H2A.Z C-terminal docking domain.
Molecular and cellular biology
GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data.
BMC bioinformatics
Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress.
Proceedings of the National Academy of Sciences of the United States of America
Improved functional overview of protein complexes using inferred epistatic relationships.
BMC systems biology
SNX27 mediates retromer tubule entry and endosome-to-plasma membrane trafficking of signalling receptors.
Nature cell biology
Imputing and predicting quantitative genetic interactions in epistatic MAPs.
Methods in molecular biology (Clifton, N.J.)
Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action.
Molecular systems biology
Rewiring of genetic networks in response to DNA damage.
Science (New York, N.Y.)
Individual lysine acetylations on the N terminus of Saccharomyces cerevisiae H2A.Z are highly but not differentially regulated.
The Journal of biological chemistry
Epistatic relationships reveal the functional organization of yeast transcription factors.
Molecular systems biology
Purification and characterization of HIV-human protein complexes.
Methods (San Diego, Calif.)
A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers.
Molecular systems biology
A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking.
Nature structural & molecular biology
Quantitative genetic interaction mapping using the E-MAP approach.
Methods in enzymology
HIV Nef is secreted in exosomes and triggers apoptosis in bystander CD4+ T cells.
Traffic (Copenhagen, Denmark)
Genome-wide association data reveal a global map of genetic interactions among protein complexes.
PLoS genetics
An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe.
Nature structural & molecular biology
A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300.
RNA (New York, N.Y.)
An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell.
Molecular systems biology
Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species.
PLoS biology
An rtt109-independent role for vps75 in transcription-associated nucleosome dynamics.
Molecular and cellular biology
Thioredoxin-related Protein 32 is an arsenite-regulated Thiol Reductase of the proteasome 19 S particle.
The Journal of biological chemistry
Learning a prior on regulatory potential from eQTL data.
PLoS genetics
A complex-based reconstruction of the Saccharomyces cerevisiae interactome.
Molecular & cellular proteomics : MCP
Systematic characterization of the protein interaction network and protein complexes in Saccharomyces cerevisiae using tandem affinity purification and mass spectrometry.
Methods in molecular biology (Clifton, N.J.)
A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing.
Molecular cell
Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment.
Genome biology
Functional targeting of DNA damage to a nuclear pore-associated SUMO-dependent ubiquitin ligase.
Science (New York, N.Y.)
Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast.
Science (New York, N.Y.)
Optimal stepwise experimental design for pairwise functional interaction studies.
Bioinformatics (Oxford, England)
A comprehensive strategy enabling high-resolution functional analysis of the yeast genome.
Nature methods
Ensemble non-negative matrix factorization methods for clustering protein-protein interactions.
Bioinformatics (Oxford, England)
Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109.
Molecular and cellular biology
BAC to the future: functional genomics in mammals.
Nature methods
Functional maps of protein complexes from quantitative genetic interaction data.
PLoS computational biology
High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombe.
Nature methods
Mutations in yhiT enable utilization of exogenous pyrimidine intermediates in Salmonella enterica serovar Typhimurium.
Microbiology (Reading, England)
H2B ubiquitylation acts as a barrier to Ctk1 nucleosomal recruitment prior to removal by Ubp8 within a SAGA-related complex.
Molecular cell
Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast.
Molecular systems biology
SIN-fully silent: HDAC complexes in fission yeast.
Nature structural & molecular biology
Backup without redundancy: genetic interactions reveal the cost of duplicate gene loss.
Molecular systems biology
CCR4/NOT complex associates with the proteasome and regulates histone methylation.
Proceedings of the National Academy of Sciences of the United States of America
Investigating the in vivo activity of the DeaD protein using protein-protein interactions and the translational activity of structured chloramphenicol acetyltransferase mRNAs.
Journal of cellular biochemistry
Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae.
Molecular & cellular proteomics : MCP
Quantitative genetic analysis in Saccharomyces cerevisiae using epistatic miniarray profiles (E-MAPs) and its application to chromatin functions.
Methods (San Diego, Calif.)
The RNA polymerase II kinase Ctk1 regulates positioning of a 5' histone methylation boundary along genes.
Molecular and cellular biology
GammaH2AX and its role in DNA double-strand break repair.
Biochemistry and cell biology = Biochimie et biologie cellulaire
PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs.
BMC bioinformatics
Signals and systems.
Genome biology
A genome-wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator.
Cell
The Saccharomyces cerevisiae histone H2A variant Htz1 is acetylated by NuA4.
Genes & development
Systems-level analyses identify extensive coupling among gene expression machines.
Molecular systems biology
A strategy for extracting and analyzing large-scale quantitative epistatic interaction data.
Genome biology
Functional genomics of the yeast DNA-damage response.
Genome biology
A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery.
Nature
Identification and characterization of Elf1, a conserved transcription elongation factor in Saccharomyces cerevisiae.
Molecular and cellular biology
BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complex.
Current biology : CB
Esf2p, a U3-associated factor required for small-subunit processome assembly and compaction.
Molecular and cellular biology
Maintenance of low histone ubiquitylation by Ubp10 correlates with telomere-proximal Sir2 association and gene silencing.
Molecular cell
The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism.
The Journal of biological chemistry
Interaction network containing conserved and essential protein complexes in Escherichia coli.
Nature
H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex.
Molecular and cellular biology
Histone H2B ubiquitylation is associated with elongating RNA polymerase II.
Molecular and cellular biology
INO80 and gamma-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair.
Cell
The functional landscape of mouse gene expression.
Journal of biology
Interaction of Fcp1 phosphatase with elongating RNA polymerase II holoenzyme, enzymatic mechanism of action, and genetic interaction with elongator.
The Journal of biological chemistry
Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4.
Proceedings of the National Academy of Sciences of the United States of America
Bromodomain factor 1 (Bdf1) is phosphorylated by protein kinase CK2.
Molecular and cellular biology
Escherichia coli mRNAs with strong Shine/Dalgarno sequences also contain 5' end sequences complementary to domain # 17 on the 16S ribosomal RNA.
Biochemical and biophysical research communications
ESF1 is required for 18S rRNA synthesis in Saccharomyces cerevisiae.
Nucleic acids research
Global mapping of the yeast genetic interaction network.
Science (New York, N.Y.)
The ctf13-30/CTF13 genomic haploinsufficiency modifier screen identifies the yeast chromatin remodeling complex RSC, which is required for the establishment of sister chromatid cohesion.
Molecular and cellular biology
A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1.
Molecular cell
A Bayesian networks approach for predicting protein-protein interactions from genomic data.
Science (New York, N.Y.)
Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II.
Molecular and cellular biology
Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter.
Molecular cell
RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach.
Molecular and cellular biology
COMPASS, a histone H3 (Lysine 4) methyltransferase required for telomeric silencing of gene expression.
The Journal of biological chemistry
Characterization of a six-subunit holo-elongator complex required for the regulated expression of a group of genes in Saccharomyces cerevisiae.
Molecular and cellular biology
COMPASS: a complex of proteins associated with a trithorax-related SET domain protein.
Proceedings of the National Academy of Sciences of the United States of America