
Research Interests: Systems biology, quantitative unbiased approaches, proteomics, genetic interactions, proteinprotein interactions, post-translational modifications, cancer, infectious diseases, cardiac development, psychiatric disorders. Summary: Our research focuses on fundamental biological mechanisms, because cures to many diseases have been revealed by unexpected discoveries in the basic sciences. We use and develop complementing technologies that allow the unbiased study of the cell. We create maps to study how proteins work together in cells, and how this changes during different diseases, including infectious diseases, cancer as well as neurological and psychiatric disorders. We strongly believe that impactful research is accomplished when diverse groups of scientists work together, and therefore we are working in close collaboration with national and international experts from different disciplines on all of our projects.
Publications
Redefining druggable targets with artificial intelligence.
Coronavirus protein interaction mapping in bat and human cells identifies molecular and genetic switches for immune evasion and replication.
Ebola virus VP35 NNLNS motif modulates viral RNA synthesis and MIB2-mediated signaling.
Programmable translational inhibition by a molecular glue-oligonucleotide conjugate.
Inference of differential kinase interaction networks with KINference.
A transcriptomic, proteomic, and functional genetic atlas dissects neurofibromin function in the peripheral nervous system.
Paracrine Signals from HIV-1 Infected Immune Cells Reprogram Cervical Cancer Pathways.
AlphaFold models of host-pathogen interactions elucidate the prevalence and structural modes of molecular mimicry.
The Mediator Kinase Module regulates cell cycle re-entry and transcriptional responses following DNA damage.
Selective RNA sequestration in biomolecular condensates directs cell fate transitions.
Structure-based discovery of highly bioavailable, covalent, broad-spectrum coronavirus MPro inhibitors with potent in vivo efficacy.
The Chlamydia effector Dre1 binds dynactin to reposition host organelles during infection.
Enhanced RNA replication and pathogenesis in recent SARS-CoV-2 variants harboring the L260F mutation in NSP6.
Lysosomal proteomics reveals mechanisms of neuronal apoE4associated lysosomal dysfunction.
Affinity Purification Mass Spectrometry on the Orbitrap-Astral Mass Spectrometer Enables High-Throughput Protein-Protein Interaction Mapping.
Coupled equilibria of dimerization and lipid binding modulate SARS Cov 2 Orf9b interactions and interferon response.
EGFR and EGFRvIII coopt host defense pathways, promoting progression in glioblastoma.
Malaria exposure remodels the plasma proteome of Ghanaian children.
Tax1bp1 enhances bacterial virulence and promotes inflammatory responses during Mycobacterium tuberculosis infection of alveolar macrophages.
A Perturbation Cell Atlas of Human Induced Pluripotent Stem Cells.
Protocol for mapping differential protein-protein interaction networks using affinity purification-mass spectrometry.
Institutional Conversion to Energy-Efficient Ultra-Low Freezers Decreases Carbon Footprint and Reduces Energy Costs.
MerlinS13 phosphorylation regulates meningioma Wnt signaling and magnetic resonance imaging features.
The Mac1 ADP-ribosylhydrolase is a Therapeutic Target for SARS-CoV-2.
Parallel genetic screens identify nuclear envelope homeostasis as a key determinant of telomere entanglement resolution in fission yeast.
A proximity proteomics pipeline with improved reproducibility and throughput.
Fate of telomere entanglements is dictated by the timing of anaphase midregion nuclear envelope breakdown.
The Chlamydia trachomatis Inc Tri1 interacts with TRAF7 to displace native TRAF7 interacting partners.
Predicted mechanistic impacts of human protein missense variants.
Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines.
An automated proximity proteomics pipeline for subcellular proteome and protein interaction mapping.
Global mapping of the Chlamydia trachomatis conventional secreted effector - host interactome reveals CebN interacts with nucleoporins and Rae1 to impede STAT1 nuclear translocation.
ATG7(2) Interacts With Metabolic Proteins and Regulates Central Energy Metabolism.
Protein interaction map of APOBEC3 enzyme family reveals deamination-independent role in cellular function.
Profiling the proximal proteome of the activated μ-opioid receptor.
Spatial control of sensory adaptation modulates mechanosensing in Pseudomonas aeruginosa.
The Chlamydia trachomatis Inc Tri1 interacts with TRAF7 to displace native TRAF7 interacting partners.
A foundational atlas of autism protein interactions reveals molecular convergence.
Protein interaction map of APOBEC3 enzyme family reveals deamination-independent role in cellular function.
Epigenetic reprogramming shapes the cellular landscape of schwannoma.
Cross-family small GTPase ubiquitination by the intracellular pathogen Legionella pneumophila.
Molecular determinants of the crosstalk between endosomal microautophagy and chaperone-mediated autophagy.
A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response.
The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5.
High-throughput chemogenetic drug screening reveals PKC-RhoA/PKN as a targetable signaling vulnerability in GNAQ-driven uveal melanoma.
Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets.
Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis.
A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication in vivo.
Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping.
Network modeling suggests HIV infection phenocopies PI3K-AKT pathway mutations to enhance HPV-associated cervical cancer.
Cross-family small GTPase ubiquitination by the intracellular pathogen Legionella pneumophila.
Functional analysis of a common BAG3 allele associated with protection from heart failure.
Structural insights into regulation of the PEAK3 pseudokinase scaffold by 14-3-3.
Lessons learned for pandemic preparedness: A collaborative network is imperative.
Defining blood-induced microglia functions in neurodegeneration through multiomic profiling.
Dengue virus NS5 degrades ERC1 during infection to antagonize NF-kB activation.
A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis in vivo.
Quantitative Proteomic Analysis Reveals apoE4-Dependent Phosphorylation of the Actin-Regulating Protein VASP.
MerlinS13 phosphorylation controls meningioma Wnt signaling and magnetic resonance imaging features.
Next-generation interaction proteomics for quantitative Jumbophage-bacteria interaction mapping.
Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13.
Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13.
Oncogenic PKA signaling increases c-MYC protein expression through multiple targetable mechanisms.
Workshop-based learning and networking: a scalable model for research capacity strengthening in low- and middle-income countries.
Quantitative proteomic analysis reveals apoE4-dependent phosphorylation of the actin regulating protein VASP.
Abstract B016: Inhibition of KRASG12C in colon cancer illustrates a link between beta-catenin, WNK, and the GID complex.
Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis.
EPCO-01. EPIGENETIC REPROGRAMMING SHAPES THE MOLECULAR AND CELLULAR LANDSCAPE OF SCHWANNOMA.
Resistance to ATR Inhibitors Is Mediated by Loss of the Nonsense-Mediated Decay Factor UPF2.
Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication.
Structure-function analysis of enterovirus protease 2A in complex with its essential host factor SETD3.
Correction: Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer.
Editor's Note: Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer.
A Whole-Genome CRISPR Screen Identifies AHR Loss as a Mechanism of Resistance to a PARP7 Inhibitor.
DLX1 and the NuRD complex cooperate in enhancer decommissioning and transcriptional repression.
Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities.
Integrative structure determination of histones H3 and H4 using genetic interactions.
A functional map of HIV-host interactions in primary human T cells.
The E3 ligase TRIM1 ubiquitinates LRRK2 and controls its localization, degradation, and toxicity.
The RNA helicase DHX16 recognizes specific viral RNA to trigger RIG-I-dependent innate antiviral immunity.
Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication.
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.
From systems to structure - using genetic data to model protein structures.
Preclinical and randomized phase I studies of plitidepsin in adults hospitalized with COVID-19.
Comparative Analysis of T-Cell Spatial Proteomics and the Influence of HIV Expression.
SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein.
Therapeutic implications of activating noncanonical PIK3CA mutations in head and neck squamous cell carcinoma.
Viral E Protein Neutralizes BET Protein-Mediated Post-Entry Antagonism of SARS-CoV-2.
Caveolin-1 and Sox-2 are predictive biomarkers of cetuximab response in head and neck cancer.
A protein interaction landscape of breast cancer.
A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity.
Interpretation of cancer mutations using a multiscale map of protein systems.
Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy.
Target Discovery for Host-Directed Antiviral Therapies: Application of Proteomics Approaches.
An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia.
Characterization of an A3G-VifHIV-1-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host-Pathogen Complexes.
Non-canonical proline-tyrosine interactions with multiple host proteins regulate Ebola virus infection.
A ciliopathy complex builds distal appendages to initiate ciliogenesis.
An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia.
Drug-induced phospholipidosis confounds drug repurposing for SARS-CoV-2.
Endosomal cAMP production broadly impacts the cellular phosphoproteome.
Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant.
Plitidepsin has a positive therapeutic index in adult patients with COVID-19 requiring hospitalization.
Adhesion-mediated mechanosignaling forces mitohormesis.
Chemical-genetic interrogation of RNA polymerase mutants reveals structure-function relationships and physiological tradeoffs.
CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.
CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.
Efficient generation of isogenic primary human myeloid cells using CRISPR-Cas9 ribonucleoproteins.
Smoothened transduces Hedgehog signals via activity-dependent sequestration of PKA catalytic subunits.
Phospholipidosis is a shared mechanism underlying the in vitro antiviral activity of many repurposed drugs against SARS-CoV-2.
Host-directed therapies against early-lineage SARS-CoV-2 retain efficacy against B.1.1.7 variant.
Evaluating a New Class of AKT/mTOR Activators for HIV Latency Reversing Activity Ex Vivo and In Vivo.
Plitidepsin has potent preclinical efficacy against SARS-CoV-2 by targeting the host protein eEF1A.
Proteomic Approaches to Study SARS-CoV-2 Biology and COVID-19 Pathology.
Mass spectrometry-based protein-protein interaction networks for the study of human diseases.
Genetic interaction mapping informs integrative structure determination of protein complexes.
An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike.
SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling.
Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.
Functional genomic screens identify human host factors for SARS-CoV-2 and common cold coronaviruses.
Evaluation of SARS-CoV-2 serology assays reveals a range of test performance.
SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells.
An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation.
Structural basis of CD4 downregulation by HIV-1 Nef.
Correction: Thioredoxin-related protein 32 is an arsenite-regulated thiol reductase of the proteasome 19 S particle.
Unbiased Proteomic Profiling Uncovers a Targetable GNAS/PKA/PP2A Axis in Small Cell Lung Cancer Stem Cells.
The Landscape of Human Cancer Proteins Targeted by SARS-CoV-2.
Test performance evaluation of SARS-CoV-2 serological assays.
mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1.
A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing.
Cyclophilin A Prevents HIV-1 Restriction in Lymphocytes by Blocking Human TRIM5α Binding to the Viral Core.
A Quantitative Genetic Interaction Map of HIV Infection.
A systems approach to infectious disease.
The functional landscape of the human phosphoproteome.
Mutations in ANKLE2, a ZIKA Virus Target, Disrupt an Asymmetric Cell Division Pathway in Drosophila Neuroblasts to Cause Microcephaly.
Systematic Identification of Host Cell Regulators of Legionella pneumophila Pathogenesis Using a Genome-wide CRISPR Screen.
Enterovirus pathogenesis requires the host methyltransferase SETD3.
Regulation of Skn7-dependent, oxidative stress-induced genes by the RNA polymerase II-CTD phosphatase, Fcp1, and Mediator kinase subunit, Cdk8, in yeast.
Synthetic Essentiality of Metabolic Regulator PDHK1 in PTEN-Deficient Cells and Cancers.
Large dataset enables prediction of repair after CRISPR-Cas9 editing in primary T cells.
PEAK3/C19orf35 pseudokinase, a new NFK3 kinase family member, inhibits CrkII through dimerization.
Mapping the protein-protein and genetic interactions of cancer to guide precision medicine.
Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis.
ARIH2 Is a Vif-Dependent Regulator of CUL5-Mediated APOBEC3G Degradation in HIV Infection.
Heart failure drug proscillaridin A targets MYC overexpressing leukemia through global loss of lysine acetylation.
Chaperone-mediated reflux of secretory proteins to the cytosol during endoplasmic reticulum stress.
Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins.
SIRT3 controls brown fat thermogenesis by deacetylation regulation of pathways upstream of UCP1.
Identification of antiviral roles for the exon-junction complex and nonsense-mediated decay in flaviviral infection.
CRISPR-Cas9 genome engineering of primary CD4+ T cells for the interrogation of HIV-host factor interactions.
Neuronal Apolipoprotein E4 Expression Results in Proteome-Wide Alterations and Compromises Bioenergetic Capacity by Disrupting Mitochondrial Function.
TCO, a Putative Transcriptional Regulator in Arabidopsis, Is a Target of the Protein Kinase CK2.
Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication.
Virus and host interactions critical for filoviral RNA synthesis as therapeutic targets.
The Cellular NMD Pathway Restricts Zika Virus Infection and Is Targeted by the Viral Capsid Protein.
Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus-Host Protein Network.
Influenza virus infection causes global RNAPII termination defects.
CRL4AMBRA1 targets Elongin C for ubiquitination and degradation to modulate CRL5 signaling.
An Mtb-Human Protein-Protein Interaction Map Identifies a Switch between Host Antiviral and Antibacterial Responses.
Sympathetic inputs regulate adaptive thermogenesis in brown adipose tissue through cAMP-Salt inducible kinase axis.
Author Correction: SMARCA2-regulated host cell factors are required for MxA restriction of influenza A viruses.
The H3K36me2 Methyltransferase Nsd1 Demarcates PRC2-Mediated H3K27me2 and H3K27me3 Domains in Embryonic Stem Cells.
SIRT1 Deacetylates Tau and Reduces Pathogenic Tau Spread in a Mouse Model of Tauopathy.
Proteome Imbalance of Mitochondrial Electron Transport Chain in Brown Adipocytes Leads to Metabolic Benefits.
How many human proteoforms are there?
Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer.
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.
Genetic Interaction Score (S-Score) Calculation, Clustering, and Visualization of Genetic Interaction Profiles for Yeast.
High-Throughput Quantitative Genetic Interaction Mapping in the Fission Yeast Schizosaccharomyces pombe.
SMARCA2-regulated host cell factors are required for MxA restriction of influenza A viruses.
Fab-based inhibitors reveal ubiquitin independent functions for HIV Vif neutralization of APOBEC3 restriction factors.
DNA Preparation from Schizosaccharomyces pombe.
Transformation of Schizosaccharomyces pombe in a 96-Well Format.
Evolutionary Proteomics Uncovers Ancient Associations of Cilia with Signaling Pathways.
Metabolic reprogramming of human CD8+ memory T cells through loss of SIRT1.
Mutations in the X-linked ATP6AP2 cause a glycosylation disorder with autophagic defects.
The Host E3-Ubiquitin Ligase TRIM6 Ubiquitinates the Ebola Virus VP35 Protein and Promotes Virus Replication.
Virus-Like Vesicles of Kaposi's Sarcoma-Associated Herpesvirus Activate Lytic Replication by Triggering Differentiation Signaling.
The Tyrosine Kinase Inhibitor Gefitinib Restricts Mycobacterium tuberculosis Growth through Increased Lysosomal Biogenesis and Modulation of Cytokine Signaling.
SMYD2-Mediated Histone Methylation Contributes to HIV-1 Latency.
The histone variant H2A.Z promotes splicing of weak introns.
PJA2 ubiquitinates the HIV-1 Tat protein with atypical chain linkages to activate viral transcription.
Systems-based analysis of RIG-I-dependent signalling identifies KHSRP as an inhibitor of RIG-I receptor activation.
A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors.
The mTOR Complex Controls HIV Latency.
G Protein-Coupled Receptor Endocytosis Confers Uniformity in Responses to Chemically Distinct Ligands.
A Herpesvirus Protein Selectively Inhibits Cellular mRNA Nuclear Export.
Combined Action of Histone Reader Modules Regulates NuA4 Local Acetyltransferase Function but Not Its Recruitment on the Genome.
A Cas9 Ribonucleoprotein Platform for Functional Genetic Studies of HIV-Host Interactions in Primary Human T Cells.
The Dengue Virus NS5 Protein Intrudes in the Cellular Spliceosome and Modulates Splicing.
A Chemical-Genomic Screen of Neglected Antibiotics Reveals Illicit Transport of Kasugamycin and Blasticidin S.
Non-degradative Ubiquitination of Protein Kinases.
A scaffold protein connects type IV pili with the Chp chemosensory system to mediate activation of virulence signaling in Pseudomonas aeruginosa.
Nonsense-mediated decay regulates key components of homologous recombination.
CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs.
Meta- and Orthogonal Integration of Influenza "OMICs" Data Defines a Role for UBR4 in Virus Budding.
CDK11 in TREX/THOC Regulates HIV mRNA 3' End Processing.
Discovery and functional characterization of a neomorphic PTEN mutation.
Critical role of acetylation in tau-mediated neurodegeneration and cognitive deficits.
Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes.
Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells.
Comparative mapping of host-pathogen protein-protein interactions.
Global Mapping of the Inc-Human Interactome Reveals that Retromer Restricts Chlamydia Infection.
Spindle Checkpoint Factors Bub1 and Bub2 Promote DNA Double-Strand Break Repair by Nonhomologous End Joining.
Differential genetic interactions of yeast stress response MAPK pathways.
Genetic interaction mapping reveals a role for the SWI/SNF nucleosome remodeler in spliceosome activation in fission yeast.
Genetic Interaction Landscape Reveals Critical Requirements for Schizosaccharomyces pombe Brc1 in DNA Damage Response Mutants.
Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST.
A combined proteomics/genomics approach links hepatitis C virus infection with nonsense-mediated mRNA decay.
Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes.
Linking tumor mutations to drug responses via a quantitative chemical-genetic interaction map.
Regulation of Sufu activity by p66β and Mycbp provides new insight into vertebrate Hedgehog signaling.
Cyclin-dependent kinase 12 increases 3' end processing of growth factor-induced c-FOS transcripts.
Acetylome profiling reveals overlap in the regulation of diverse processes by sirtuins, gcn5, and esa1.
Quantitative analysis of triple-mutant genetic interactions.
Yeast X-chromosome-associated protein 5 (Xap5) functions with H2A.Z to suppress aberrant transcripts.
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.
Adventures in time and space: splicing efficiency and RNA polymerase II elongation rate.
Conditional genetic interactions of RTT107, SLX4, and HRQ1 reveal dynamic networks upon DNA damage in S. cerevisiae.
A chaperone-assisted degradation pathway targets kinetochore proteins to ensure genome stability.
A Pil1-Sle1-Syj1-Tax4 functional pathway links eisosomes with PI(4,5)P2 regulation.
AFF1 is a ubiquitous P-TEFb partner to enable Tat extraction of P-TEFb from 7SK snRNP and formation of SECs for HIV transactivation.
Evolution and functional cross-talk of protein post-translational modifications.
IFI16 DNA sensor is required for death of lymphoid CD4 T cells abortively infected with HIV.
High-resolution network biology: connecting sequence with function.
High-throughput genetic and gene expression analysis of the RNAPII-CTD reveals unexpected connections to SRB10/CDK8.
From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II.
A lipid E-MAP identifies Ubx2 as a critical regulator of lipid saturation and lipid bilayer stress.
Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.
Bringing it all together: big data and HIV research.
Quantitative genetic-interaction mapping in mammalian cells.
From systems to structure: bridging networks and mechanism.
CBFβ stabilizes HIV Vif to counteract APOBEC3 at the expense of RUNX1 target gene expression.
Dispersed sites of HIV Vif-dependent polyubiquitination in the DNA deaminase APOBEC3F.
A gene ontology inferred from molecular networks.
All or nothing: protein complexes flip essentiality between distantly related eukaryotes.
HIV-1 Tat recruits transcription elongation factors dispersed along a flexible AFF4 scaffold.
Inhibition of RNA lariat debranching enzyme suppresses TDP-43 toxicity in ALS disease models.
Replication fork collapse and genome instability in a deoxycytidylate deaminase mutant.
Moloney leukemia virus type 10 inhibits reverse transcription and retrotransposition of intracisternal a particles.
Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal.
Differential network biology.
First-in-class small molecule inhibitors of the single-strand DNA cytosine deaminase APOBEC3G.
Comparative interaction networks: bridging genotype to phenotype.
Host cell interactome of HIV-1 Rev includes RNA helicases involved in multiple facets of virus production.
RNA polymerase II carboxyl-terminal domain phosphorylation regulates protein stability of the Set2 methyltransferase and histone H3 di- and trimethylation at lysine 36.
Eisosome proteins assemble into a membrane scaffold.
Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs.
Key functional regions in the histone variant H2A.Z C-terminal docking domain.
GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data.
Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress.
Improved functional overview of protein complexes using inferred epistatic relationships.
SNX27 mediates retromer tubule entry and endosome-to-plasma membrane trafficking of signalling receptors.
Imputing and predicting quantitative genetic interactions in epistatic MAPs.
Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action.
Rewiring of genetic networks in response to DNA damage.
Individual lysine acetylations on the N terminus of Saccharomyces cerevisiae H2A.Z are highly but not differentially regulated.
Epistatic relationships reveal the functional organization of yeast transcription factors.
Purification and characterization of HIV-human protein complexes.
A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers.
A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking.
Quantitative genetic interaction mapping using the E-MAP approach.
HIV Nef is secreted in exosomes and triggers apoptosis in bystander CD4+ T cells.
Genome-wide association data reveal a global map of genetic interactions among protein complexes.
An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe.
A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300.
An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell.
Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species.
An rtt109-independent role for vps75 in transcription-associated nucleosome dynamics.
Thioredoxin-related Protein 32 is an arsenite-regulated Thiol Reductase of the proteasome 19 S particle.
Learning a prior on regulatory potential from eQTL data.
A complex-based reconstruction of the Saccharomyces cerevisiae interactome.
Systematic characterization of the protein interaction network and protein complexes in Saccharomyces cerevisiae using tandem affinity purification and mass spectrometry.
A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing.
Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment.
Functional targeting of DNA damage to a nuclear pore-associated SUMO-dependent ubiquitin ligase.
Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast.
Optimal stepwise experimental design for pairwise functional interaction studies.
A comprehensive strategy enabling high-resolution functional analysis of the yeast genome.
Ensemble non-negative matrix factorization methods for clustering protein-protein interactions.
Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109.
BAC to the future: functional genomics in mammals.
Functional maps of protein complexes from quantitative genetic interaction data.
High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombe.
Mutations in yhiT enable utilization of exogenous pyrimidine intermediates in Salmonella enterica serovar Typhimurium.
H2B ubiquitylation acts as a barrier to Ctk1 nucleosomal recruitment prior to removal by Ubp8 within a SAGA-related complex.
Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast.
SIN-fully silent: HDAC complexes in fission yeast.
Backup without redundancy: genetic interactions reveal the cost of duplicate gene loss.
CCR4/NOT complex associates with the proteasome and regulates histone methylation.
Investigating the in vivo activity of the DeaD protein using protein-protein interactions and the translational activity of structured chloramphenicol acetyltransferase mRNAs.
Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae.
Quantitative genetic analysis in Saccharomyces cerevisiae using epistatic miniarray profiles (E-MAPs) and its application to chromatin functions.
The RNA polymerase II kinase Ctk1 regulates positioning of a 5' histone methylation boundary along genes.
GammaH2AX and its role in DNA double-strand break repair.
PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs.
Signals and systems.
A genome-wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator.
The Saccharomyces cerevisiae histone H2A variant Htz1 is acetylated by NuA4.
Systems-level analyses identify extensive coupling among gene expression machines.
A strategy for extracting and analyzing large-scale quantitative epistatic interaction data.
Functional genomics of the yeast DNA-damage response.
A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery.
Identification and characterization of Elf1, a conserved transcription elongation factor in Saccharomyces cerevisiae.
BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complex.
Esf2p, a U3-associated factor required for small-subunit processome assembly and compaction.
Maintenance of low histone ubiquitylation by Ubp10 correlates with telomere-proximal Sir2 association and gene silencing.
The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism.
Interaction network containing conserved and essential protein complexes in Escherichia coli.
H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex.
Histone H2B ubiquitylation is associated with elongating RNA polymerase II.
INO80 and gamma-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair.
The functional landscape of mouse gene expression.
Interaction of Fcp1 phosphatase with elongating RNA polymerase II holoenzyme, enzymatic mechanism of action, and genetic interaction with elongator.
Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4.
Bromodomain factor 1 (Bdf1) is phosphorylated by protein kinase CK2.
Escherichia coli mRNAs with strong Shine/Dalgarno sequences also contain 5' end sequences complementary to domain # 17 on the 16S ribosomal RNA.
ESF1 is required for 18S rRNA synthesis in Saccharomyces cerevisiae.
Global mapping of the yeast genetic interaction network.
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.
A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1.
A Bayesian networks approach for predicting protein-protein interactions from genomic data.
Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II.
Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter.
RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach.
COMPASS, a histone H3 (Lysine 4) methyltransferase required for telomeric silencing of gene expression.
Characterization of a six-subunit holo-elongator complex required for the regulated expression of a group of genes in Saccharomyces cerevisiae.
COMPASS: a complex of proteins associated with a trithorax-related SET domain protein.
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