Edward M. Marcotte

The paper predicts the structure of the CPLANE complex and identifies novel interactors of Jbts17, revealing its role in ciliogenesis through in silico and experimental validation.

This study provides a genomic, transcriptomic, and proteomic analysis of wax synthesis in Dactylopius opuntiae, identifying 26 FAR genes and their evolutionary expansion.

This paper introduces a deep learning model that predicts biological function from chemical structure using scientific literature, identifying effective inhibitors of beta-lactamases.

This paper identifies AtLa1 as an essential RNA-binding factor for Arabidopsis telomerase function, revealing its role in telomerase complex assembly and highlighting evolutionary conservation with yeast and ciliate proteins.

This paper introduces a computational pipeline using DNA k-mer imprints to agnostically classify and distinguish materials based on their sequence patterns.

The paper identifies novel membrane-bound transcriptional regulators by analyzing rare, evolutionarily conserved domain combinations in membrane proteins.

The paper reconstructs the protein interactome of the Last Eukaryotic Common Ancestor and identifies new human gene-disease associations for bone density and congenital birth defects.

The paper identifies key trafficking components involved in ERECTA receptor kinase signaling that regulate plant stomatal development through endocytosis.

This paper introduces an expectation maximization framework for inferring protein abundances from fluorosequencing data, showing significant improvements in accuracy and scalability.

The paper identifies two proteins, Ccdc78 and Ccdc33, at the distal tip of vertebrate motile cilia, showing they are essential for cilia organization, length regulation, and function.

The paper identifies and characterizes a new conserved protein complex, CAGE, found in both prokaryotes and eukaryotes, revealing its structural features and evolutionary distribution.

The paper investigates the role of Lrrc56 in vertebrate multiciliated cells, showing it regulates outer dynein arm deployment through interaction with Odad3, linking LRRC56 mutations to primary ciliary dyskinesia.

This study identifies RSG1/CPLANE2 as a causative gene for human ciliopathy and shows its role in ciliary transition zone assembly.

The paper uses cryo-electron tomography to study the structure of full-length EGFR in extracellular vesicles, revealing its clustering and signaling domain positioning.

VerteBrain maps conserved brain protein interactions across five vertebrate species, revealing novel complexes and disease mechanisms.

This study uses shotgun-EM to identify and characterize three protein complexes, including the first experimentally determined structure of Pks16 in D. discoideum.

The paper develops a method to detect combinatorial phosphorylation patterns on RNA polymerase II CTD and shows they recruit TREX for mRNA processing and export.

The paper identifies proteoform truncations in human and plant proteomes and describes their functional implications and evolutionary conservation.

DeepSLICEM improves clustering of cryo-EM 2D projections by combining image and graph features, achieving better accuracy than previous methods on synthetic and experimental datasets.

The paper systematically profiles protein dynamics in ale yeast during fermentation and repitching, identifying changes in ergosterol and isobutyraldehyde metabolism.

This paper improves fluorosequencing by optimizing fluorophores, reducing dye interactions, and creating an end-to-end workflow, demonstrating its potential for high-sensitivity clinical proteomics.

The paper uses reinforcement learning to detect protein complexes in PPI networks, identifying 1,157 complexes with improved speed and accuracy compared to existing methods.

The paper develops and compares two methods to estimate error rates in single molecule protein sequencing experiments, finding that one method outperforms the other in most criteria.

The paper introduces whatprot, a hybrid kNN-HMM classifier for amino acid sequence assignment from fluorosequencing data, improving precision and recall over individual methods.

The paper tests if AlphaFold2 accurately models intracellular protein conformations using cross-linking mass spectrometry of endogenous ciliary proteins in Tetrahymena thermophila.

The paper analyzes proteomic changes in Arabidopsis hybrids and allotetraploids, finding nonadditive protein expression and increased solubility of photosynthetic proteins associated with hybrid vigor.

The paper develops yeast biosensors for CB1R and CB2R to screen cannabinoids and identify structure-activity relationships.

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

The paper introduces MERGE, a method for marker-less, scalable genome editing in yeast by combining CRISPR-Cas9 and gene drives to efficiently integrate and combine multiple genetic edits.

This study engineers yeast to produce cholesterol, enabling functional expression of human opioid and other GPCRs, creating biosensors with measurable agonist responses and antagonist inhibition.