List of works - Edward Marcotte

A combined algorithm for genome-wide prediction of protein function

scientific article (publication date: 4 November 1999)

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

scientific article

A fast algorithm for genome-wide analysis of proteins with repeated sequences.

scientific article published on June 1999

A fast coarse filtering method for peptide identification by mass spectrometry.

scientific article

A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality.

scientific article

A highly parallel strategy for storage of digital information in living cells

scientific article published on 17 October 2018

A liquid-like organelle at the root of motile ciliopathy

scientific article published on 18 December 2018

A probabilistic functional network of yeast genes

scientific article published on 01 November 2004

A probabilistic view of gene function.

scientific article published on June 2004

A proteomic survey of widespread protein aggregation in yeast.

scientific article

A self-assembling lanthanide molecular nanoparticle for optical imaging

scientific article

A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans.

scientific article published on 27 January 2008

A synthetic genetic edge detection program.

scientific article published on June 2009

A theoretical justification for single molecule peptide sequencing

scientific article (publication date: February 2015)

Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation.

scientific article

Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence

scientific article

An open invitation to the Understudied Proteins Initiative

scientific article published on 9 May 2022

Ancestral reconstruction of protein interaction networks

scientific article published on 28 October 2019

Applications of comparative evolution to human disease genetics

scientific article

Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness

scientific article

Bioinformatic challenges for the next decade(s).

scientific article

Characterising and predicting haploinsufficiency in the human genome.

scientific article

Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum.

scientific article

Chitinases, chitosanases, and lysozymes can be divided into procaryotic and eucaryotic families sharing a conserved core.

scientific article published on February 1996

Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping.

scientific article

Classification of Single Particles from Human Cell Extract Reveals Distinct Structures

scientific article published on 01 July 2018

Comparative experiments on learning information extractors for proteins and their interactions.

scientific article

Comparing Protein and mRNA Abundances to Protein Expression Regulation.

scientific article published in October 2011

ComplexQuant: high-throughput computational pipeline for the global quantitative analysis of endogenous soluble protein complexes using high resolution protein HPLC and precision label-free LC/MS/MS

scientific article published on 12 October 2012

Comprehensive de Novo Peptide Sequencing from MS/MS Pairs Generated through Complementary Collision Induced Dissociation and 351 nm Ultraviolet Photodissociation.

scientific article

Computational genetics: finding protein function by nonhomology methods.

scientific article published on June 2000

Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome

scientific article

Control of cellular morphogenesis by the Ip12/Bem2 GTPase-activating protein: possible role of protein phosphorylation

scientific article

Coordinated genomic control of ciliogenesis and cell movement by RFX2.

scientific article published on 14 January 2014

Correction: Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses

scientific article published on 12 September 2013

Corrigendum: The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery.

scientific article published in July 2016

Crystallization of a chitosanase from Streptomyces N174

scientific article published on 01 August 1993

Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit.

scientific article

Development through the eyes of functional genomics.

scientific article published in August 2004

Diametrical clustering for identifying anti-correlated gene clusters.

scientific article

Dynamic reorganization of metabolic enzymes into intracellular bodies

scientific article

Effects of functional bias on supervised learning of a gene network model.

scientific article published on January 2009

Efforts to make and apply humanized yeast

scientific article

Evolutionarily repurposed networks reveal the well-known antifungal drug thiabendazole to be a novel vascular disrupting agent

scientific article

Exploiting big biology: integrating large-scale biological data for function inference.

scientific article

Exploiting the co-evolution of interacting proteins to discover interaction specificity

scientific article published on 01 March 2003

Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations

scientific article

Flaws in evaluation schemes for pair-input computational predictions.

scientific article published on December 2012

Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins

scientific article published on 02 December 2020

GWAB: a web server for the network-based boosting of human genome-wide association data.

scientific article

Genetic dissection of the biotic stress response using a genome-scale gene network for rice.

scientific article published on 31 October 2011

Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea

scientific article

Global metabolic changes following loss of a feedback loop reveal dynamic steady states of the yeast metabolome

scientific article published on 30 June 2006

Global signatures of protein and mRNA expression levels

scientific article

Group II intron protein localization and insertion sites are affected by polyphosphate

scientific article

High-Throughput Immunofluorescence Microscopy Using Yeast Spheroplast Cell-Based Microarrays ⬇️

scientific article published on January 1, 2011

Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures

scientific article published on 22 October 2018

How complete are current yeast and human protein-interaction networks?

scientific article published on January 2006

HumanNet v2: human gene networks for disease research

scientific article published on 01 January 2019

Id2a functions to limit Notch pathway activity and thereby influence the transition from proliferation to differentiation of retinoblasts during zebrafish retinogenesis ⬇️

scientific article published on September 8, 2012

Identification and characterization of the constituent human serum antibodies elicited by vaccination.

scientific article published on 27 January 2014

Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets.

scientific article published on 12 October 2017

Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy

scientific article

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

scientific article published on 13 March 2012

Integrating functional genomics data

scientific article published on 01 January 2008

Integrating shotgun proteomics and mRNA expression data to improve protein identification

scientific article

Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes

scientific article published on 8 June 2017

Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex

scientific article published in 2022

Kinetic analysis of barley chitinase.

scientific article published on August 1997

LGL: creating a map of protein function with an algorithm for visualizing very large biological networks.

scientific article published in June 2004

Label-Free Protein Quantitation Using Weighted Spectral Counting ⬇️

scientific article published on January 1, 2012

Lanthanide nano-drums: a new class of molecular nanoparticles for potential biomedical applications.

scientific article published on January 2014

Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions

scientific article

Localizing proteins in the cell from their phylogenetic profiles.

scientific article

Long-term neural and physiological phenotyping of a single human

scientific article

MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network.

scientific article

Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias.

scientific article

Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection

scientific article published on 18 September 2017

Modes of interaction between individuals dominate the topologies of real world networks

scientific article published on 20 March 2015

MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates.

scientific article

Murine Cytomegalovirus Deubiquitinase Regulates Viral Chemokine Levels To Control Inflammation and Pathogenesis

scientific article

Network Biology editorial 2013.

scientific article

Parallel evolution in Pseudomonas aeruginosa over 39,000 generations in vivo.

scientific article

Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in Xenopus

scientific article published on 10 January 2018

Photography Coupled with Self-Propagating Chemical Cascades: Differentiation and Quantitation of G- and V-Nerve Agent Mimics via Chromaticity

scientific article published on 27 June 2018

Predictability of Genetic Interactions from Functional Gene Modules

scientific article published on 22 December 2016

Predicting genetic modifier loci using functional gene networks

scientific article

Prioritizing candidate disease genes by network-based boosting of genome-wide association data.

scientific article

Protein Expression Regulation under Oxidative Stress ⬇️

scientific article published on September 20, 2011

Protein function in the post-genomic era.

scientific article

Protein function prediction using the Protein Link EXplorer (PLEX)

scientific article published on 08 February 2005

Protein interaction networks from yeast to human

scientific article (publication date: June 2004)

Protein localization screening in vivo reveals novel regulators of multiciliated cell development and function.

scientific article published on 27 November 2017

Proteomic and protein interaction network analysis of human T lymphocytes during cell-cycle entry

scientific article published on 13 March 2012

Proteomic identification of monoclonal antibodies from serum

scientific article

Pseudomonas aeruginosa enhances production of a non-alginate exopolysaccharide during long-term colonization of the cystic fibrosis lung.

scientific article

Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways.

scientific article

RFX2 is broadly required for ciliogenesis during vertebrate development.

scientific article published on 29 December 2011

RIDDLE: reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network ⬇️

scientific article published on December 26, 2012

Reducing MCM levels in human primary T cells during the G(0)-->G(1) transition causes genomic instability during the first cell cycle

scientific article published on 3 May 2010

Revisiting and revising the purinosome

scientific article

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

scientific article

Single-step Precision Genome Editing in Yeast Using CRISPR-Cas9.

scientific article

Solution-phase and solid-phase sequential, selective modification of side chains in KDYWEC and KDYWE as models for usage in single-molecule protein sequencing. ⬇️

scientific article

Sperm is epigenetically programmed to regulate gene transcription in embryos

scientific article published on 31 March 2016

Structural analysis shows five glycohydrolase families diverged from a common ancestor.

scientific article published in September 1998

Synthetic biology: engineering Escherichia coli to see light

scientific article

Systematic Identification of Protein Phosphorylation-Mediated Interactions

scientific article published on 21 January 2021

Systematic bacterialization of yeast genes identifies a near-universally swappable pathway

scientific article published on 29 June 2017

Systematic comparison of variant calling pipelines using gold standard personal exome variants

scientific article

Systematic definition of protein constituents along the major polarization axis reveals an adaptive reuse of the polarization machinery in pheromone-treated budding yeast.

scientific article published in January 2009

Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network ⬇️

scientific article published on August 25, 2011

Systematic profiling of cellular phenotypes with spotted cell microarrays reveals mating-pheromone response genes

scientific article

Systems-wide Studies Uncover Commander, a Multiprotein Complex Essential to Human Development.

scientific article published on May 2017

Temporal stability and molecular persistence of the bone marrow plasma cell antibody repertoire

scientific article published on 21 December 2016

The DEAH-box helicase Dhr1 dissociates U3 from the pre-rRNA to promote formation of the central pseudoknot.

scientific article published on 24 February 2015

The Many Nuanced Evolutionary Consequences of Duplicated Genes

scientific article published on 01 February 2019

The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery

scientific article published on 09 May 2016

The genome sequence of the filamentous fungus Neurospora crassa

scientific article

The path not taken.

scientific article

The planar cell polarity effector Fuz is essential for targeted membrane trafficking, ciliogenesis and mouse embryonic development

scientific journal article

Towards Consensus Gene Ages

scientific article published on 03 June 2016

Two-tiered approach identifies a network of cancer and liver disease-related genes regulated by miR-122.

scientific article

UVnovo: A de Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry.

scientific article

Understudied proteins: opportunities and challenges for functional proteomics

scientific article published on 9 May 2022

Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation.

scientific article

Withdrawn as Duplicate: The many nuanced evolutionary consequences of duplicated genes

scientific article published on 01 December 2018

Yeast cells expressing the human mitochondrial DNA polymerase reveal correlations between polymerase fidelity and human disease progression

scientific article published on 07 January 2014

hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies

scientific article published on 11 May 2021

List of works by Edward Marcotte

A combined algorithm for genome-wide prediction of protein function

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

A fast algorithm for genome-wide analysis of proteins with repeated sequences.

A fast coarse filtering method for peptide identification by mass spectrometry.

A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality.

A highly parallel strategy for storage of digital information in living cells

A liquid-like organelle at the root of motile ciliopathy

A probabilistic functional network of yeast genes

A probabilistic view of gene function.

A proteomic survey of widespread protein aggregation in yeast.

A self-assembling lanthanide molecular nanoparticle for optical imaging

A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans.

A synthetic genetic edge detection program.

A theoretical justification for single molecule peptide sequencing

Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation.

Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence

An open invitation to the Understudied Proteins Initiative

Ancestral reconstruction of protein interaction networks

Applications of comparative evolution to human disease genetics

Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness

Bioinformatic challenges for the next decade(s).

Characterising and predicting haploinsufficiency in the human genome.

Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum.

Chitinases, chitosanases, and lysozymes can be divided into procaryotic and eucaryotic families sharing a conserved core.

Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping.

Classification of Single Particles from Human Cell Extract Reveals Distinct Structures

Comparative experiments on learning information extractors for proteins and their interactions.

Comparing Protein and mRNA Abundances to Protein Expression Regulation.

ComplexQuant: high-throughput computational pipeline for the global quantitative analysis of endogenous soluble protein complexes using high resolution protein HPLC and precision label-free LC/MS/MS

Comprehensive de Novo Peptide Sequencing from MS/MS Pairs Generated through Complementary Collision Induced Dissociation and 351 nm Ultraviolet Photodissociation.

Computational genetics: finding protein function by nonhomology methods.

Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome

Control of cellular morphogenesis by the Ip12/Bem2 GTPase-activating protein: possible role of protein phosphorylation

Coordinated genomic control of ciliogenesis and cell movement by RFX2.

Correction: Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses

Corrigendum: The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery.

Crystallization of a chitosanase from Streptomyces N174

Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit.

Development through the eyes of functional genomics.

Diametrical clustering for identifying anti-correlated gene clusters.

Dynamic reorganization of metabolic enzymes into intracellular bodies

Effects of functional bias on supervised learning of a gene network model.

Efforts to make and apply humanized yeast

Evolutionarily repurposed networks reveal the well-known antifungal drug thiabendazole to be a novel vascular disrupting agent

Exploiting big biology: integrating large-scale biological data for function inference.

Exploiting the co-evolution of interacting proteins to discover interaction specificity

Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations

Flaws in evaluation schemes for pair-input computational predictions.

Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins

GWAB: a web server for the network-based boosting of human genome-wide association data.

Genetic dissection of the biotic stress response using a genome-scale gene network for rice.

Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea

Global metabolic changes following loss of a feedback loop reveal dynamic steady states of the yeast metabolome

Global signatures of protein and mRNA expression levels

Group II intron protein localization and insertion sites are affected by polyphosphate

High-Throughput Immunofluorescence Microscopy Using Yeast Spheroplast Cell-Based Microarrays ⬇️

Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures

How complete are current yeast and human protein-interaction networks?

HumanNet v2: human gene networks for disease research

Id2a functions to limit Notch pathway activity and thereby influence the transition from proliferation to differentiation of retinoblasts during zebrafish retinogenesis ⬇️

Identification and characterization of the constituent human serum antibodies elicited by vaccination.

Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets.

Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

Integrating functional genomics data

Integrating shotgun proteomics and mRNA expression data to improve protein identification

Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes

Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex

Kinetic analysis of barley chitinase.

LGL: creating a map of protein function with an algorithm for visualizing very large biological networks.

Label-Free Protein Quantitation Using Weighted Spectral Counting ⬇️

Lanthanide nano-drums: a new class of molecular nanoparticles for potential biomedical applications.

Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions

Localizing proteins in the cell from their phylogenetic profiles.

Long-term neural and physiological phenotyping of a single human

MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network.

Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias.

Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection

Modes of interaction between individuals dominate the topologies of real world networks