Andrew Emili

scCont is an unsupervised contrastive learning framework that extracts interpretable functional transition units from scRNA-seq data, outperforming baseline methods in capturing biologically meaningful dynamics.

The paper identifies extensive interactions among C2H2 zinc finger proteins at chromatin loop anchors using ChIP-seq, interactome data, and chromatin interaction maps.

The paper maps protein interaction network remodeling in a mouse tauopathy model using multi-omics and machine learning, identifying key complexes involved in early disease phenotypes.

The paper identifies prion synaptotoxic pathways and inhibitory drugs using phosphoproteomic and transcriptomic data from prion-treated neurons.

This study investigates age- and pathology-dependent changes in the epitranscriptome and translational dysfunction in a tauopathy mouse model, revealing significant alterations in tRNA biology and codon usage patterns.

The paper validates Zhx2 as a quantitative trait gene influencing brain oxymorphone levels and opioid behavior through genetic and multi-omics analyses in mice.

The paper develops a method to discover RNA-protein-small molecule complexes using proteome-wide stability assays and applies it to identify novel DDX helicase targets of rocaglates.

The paper compares molecular programs in Drosophila nurse cell death and clearance under different conditions, identifying pathways and genes involved in apoptotic and non-apoptotic clearance mechanisms.

This study investigates immune regulation in symbiotic and aposymbiotic coral tissue using multiomic approaches, revealing compartmentalized immune suppression in specific cell types during symbiosis.

This study shows TIA1 regulates divergent inflammatory responses in microglia and macrophages, reducing brain inflammation and tau pathology while increasing peripheral inflammation.

This study identifies aldolase A as a novel Reelin effector involved in dendritic development, independent of its glycolytic function.

The paper uses proximity labeling to study the dynamic SQSTM1 protein network and shows that aggregated tau alters its interactions with stress-associated proteins.

PANAMA enables high sensitivity joint metabolomics and proteomics analysis using nanoflow LC/MS without instrument duplication, improving resolution and detection sensitivity.

This paper develops BODIPY-based fluorescent probes for selective amino acid identification through optimized spectral and photophysical properties.

This study enhances AlphaFold for predicting phosphopeptide-protein complex structures, achieving higher accuracy in lDDT scores for peptides.

This study shows that DOT1L promotes the degradation of c-MYC and MML-1 transcription factors on chromatin, regulating their target genes and potentially offering new cancer treatment strategies.

The paper uses large-scale perturbation profiles to analyze drug mechanisms of action and polypharmacology across multiple tumor subtypes and tissues.

The paper shows that ORF57 from Human Herpesvirus 8 reduces TDP-43 aggregation and cell death by interacting with ISR components.

DESP resolves cell state contributions to bulk molecular measurements using single-cell data, demonstrating accuracy in reconstructing proteome and transcriptome signatures during epithelial-to-mesenchymal transition.

This study defines the RBC proteome and interactome using mass spectrometry and machine learning, revealing key biological processes and structural models.

The paper identifies ZFC3H1 and U1-70K as factors promoting nuclear retention of mRNAs with 5' splice site motifs in nuclear speckles through a splicing-independent mechanism.

The paper maps EMT transitions through multi-omic profiling, identifies key regulatory factors, and reveals discordance between molecular layers in human mammary epithelial cells.

The paper shows that ApoE alleles compete with mCRP for CD31 binding on brain endothelia, leading to differential AD pathology based on ApoE genotype.

This paper identifies a complex involving HNRNPA2B1, N6-methyladenosine modified transcripts, and toxic tau oligomers that mediates neurodegeneration.

This study identifies a mutation in Hnrnph1 that reduces methamphetamine-induced reinforcement, reward, and dopamine release while increasing synaptic hnRNP H and mitochondrial proteins in mice.

The paper shows that TPR is necessary for nuclear export of mRNAs and lncRNAs from intronless and intron-poor genes, with reporter constructs validating this role.

This paper demonstrates that pancreatic tumor organoids (PDOs) recapitulate PDX models' features and can identify clinically-actionable biomarkers in blood.

The paper identifies PACSIN1 as a key negative regulator of KCC2 function through a native KCC2 interactome analysis in the mouse brain.