DIP: the Database of Interacting Proteins. - Ioannis Xenarios; Danny W. Rice; Lukasz Salwínski; Marisa K. Baron; Edward M. Marcotte; David Eisenberg 001 (Nucleic Acids Res., 2000)

Exploiting Big Biology: Integrating Large-scale Biological Data for Function Inference. - Edward M. Marcotte; Shailesh V. Date (Briefings Bioinform., 2001)

Mining literature for protein-protein interactions. - Edward M. Marcotte; Ioannis Xenarios; David Eisenberg 001 (Bioinform., 2001)

DIP: The Database of Interacting Proteins: 2001 update. - Ioannis Xenarios; Esteban Fernandez 002; Lukasz Salwínski; Xiaoqun Joyce Duan; Michael J. Thompson; Edward M. Marcotte; David Eisenberg 001 (Nucleic Acids Res., 2001)

Predicting Protein Function and Nworks on a Genomewide Scale. - Edward M. Marcotte (Gene Regulations and Metabolism, 2002)

Diametrical clustering for identifying anti-correlated gene clusters. - Inderjit S. Dhillon; Edward M. Marcotte; Usman Roshan (Bioinform., 2003)

Using Biomedical Literature Mining to Consolidate the Set of Known Human Protein-Protein Interactions. - Arun K. Ramani; Razvan C. Bunescu; Raymond J. Mooney; Edward M. Marcotte (LBLODMBS@IDMB, 2005)

Comparative experiments on learning information extractors for proteins and their interactions. - Razvan C. Bunescu; Ruifang Ge; Rohit J. Kate; Edward M. Marcotte; Raymond J. Mooney; Arun K. Ramani; Yuk Wah Wong (Artif. Intell. Medicine, 2005)

Protein function prediction using the Protein Link EXplorer (PLEX). - Shailesh V. Date; Edward M. Marcotte (Bioinform., 2005)

Integrating Co-occurrence Statistics with Information Extraction for Robust Retrieval of Protein Interactions from Medline. - Razvan C. Bunescu; Raymond J. Mooney; Arun K. Ramani; Edward M. Marcotte (BioNLP@NAACL-HLT, 2006)

A fast coarse filtering method for peptide identification by mass spectrometry. - Smriti R. Ramakrishnan; Rui Mao 001; Aleksey A. Nakorchevskiy; John T. Prince; Willard S. Willard; Weijia Xu; Edward M. Marcotte; Daniel P. Miranker (Bioinform., 2006)

A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. - G. Traver Hart; Insuk Lee; Edward M. Marcotte (BMC Bioinform., 2007)

mspire: mass spectrometry proteomics in Ruby. - John T. Prince; Edward M. Marcotte (Bioinform., 2008)

The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results. - John C. Braisted; Srilatha Kuntumalla; Christine Vogel; Edward M. Marcotte; Alan R. Rodrigues; Rong Wang; Shih-Ting Huang; Erik S. Ferlanti; Alexander I. Saeed; Robert D. Fleischmann; Scott N. Peterson; Rembert Pieper (BMC Bioinform., 2008)

Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence. - Wan Kyu Kim; Edward M. Marcotte (PLoS Comput. Biol., 2008)

Mining gene functional networks to improve mass-spectrometry-based protein identification. - Smriti R. Ramakrishnan; Christine Vogel; Taejoon Kwon; Luiz O. F. Penalva; Edward M. Marcotte; Daniel P. Miranker (Bioinform., 2009)

Integrating shotgun proteomics and mRNA expression data to improve protein identification. - Smriti R. Ramakrishnan; Christine Vogel; John T. Prince; Rong Wang; Zhihua Li; Luiz O. F. Penalva; Margaret Myers; Edward M. Marcotte; Daniel P. Miranker (Bioinform., 2009)

Revisiting the negative example sampling problem for predicting protein-protein interactions. - Yungki Park; Edward M. Marcotte (Bioinform., 2011)

Label-Free Protein Quantitation Using Weighted Spectral Counting. - Christine Vogel; Edward M. Marcotte (Quantitative Methods in Proteomics, 2012)

Prediction of gene-phenotype associations in humans, mice, and plants using phenologs. - John O. Woods; Ulf Martin Singh-Blom; Jon M. Laurent; Kriston L. McGary; Edward M. Marcotte (BMC Bioinform., 2013)

MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network. - Sohyun Hwang; Eiru Kim; Sunmo Yang; Edward M. Marcotte; Insuk Lee (Nucleic Acids Res., 2014)

Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation. - John R. Houser; Craig Barnhart; Daniel R. Boutz; Sean M. Carroll; Aurko Dasgupta; Joshua K. Michener; Brittany D. Needham; Ophelia Papoulas; Viswanadham Sridhara; Dariya K. Sydykova; Christopher J. Marx; M. Stephen Trent; et al. (PLoS Comput. Biol., 2015)

A Theoretical Justification for Single Molecule Peptide Sequencing. - Jagannath Swaminathan; Alexander A. Boulgakov; Edward M. Marcotte (PLoS Comput. Biol., 2015)

Computational discovery of pathway-level genetic vulnerabilities in non-small-cell lung cancer. - Jonathan H. Young; Michael Peyton; Hyun Seok Kim; Elizabeth McMillan; John D. Minna; Michael A. White; Edward M. Marcotte (Bioinform., 2016)

MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates. - Eiru Kim; Sohyun Hwang; Hyojin Kim 002; Hongseok Shim; Byunghee Kang; Sunmo Yang; Jae Ho Shim; Seung Yeon Shin; Edward M. Marcotte; Insuk Lee (Nucleic Acids Res., 2016)

GWAB: a web server for the network-based boosting of human genome-wide association data. - Jung Eun Shim; Changbae Bang; Sunmo Yang; Tak Lee; Sohyun Hwang; Chan Yeong Kim; Ulf Martin Singh-Blom; Edward M. Marcotte; Insuk Lee (Nucleic Acids Res., 2017)

Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets. - Kevin Drew; Christian L. Müller; Richard Bonneau; Edward M. Marcotte (PLoS Comput. Biol., 2017)

HumanNet v2: human gene networks for disease research. - Sohyun Hwang; Chan Yeong Kim; Sunmo Yang; Eiru Kim; G. Traver Hart; Edward M. Marcotte; Insuk Lee (Nucleic Acids Res., 2019)

Ancestral reconstruction of protein interaction networks. - Benjamin J. Liebeskind; Richard W. Aldrich; Edward M. Marcotte (PLoS Comput. Biol., 2019)

Structural Biology in the Multi-Omics Era. - Caitlyn L. McCafferty; Eric J. Verbeke; Edward M. Marcotte; David W. Taylor (J. Chem. Inf. Model., 2020)

HumanNet v3: an improved database of human gene networks for disease research. - Chan Yeong Kim; Seungbyn Baek; Junha Cha; Sunmo Yang; Eiru Kim; Edward M. Marcotte; G. Traver Hart; Insuk Lee (Nucleic Acids Res., 2022)

Mining Patents with Large Language Models Demonstrates Congruence of Functional Labels and Chemical Structures. - Clayton W. Kosonocky; Claus O. Wilke; Edward M. Marcotte; Andrew D. Ellington (CoRR, 2023)

Amino acid sequence assignment from single molecule peptide sequencing data using a two-stage classifier. - Matthew Beauregard Smith; Zack Booth Simpson; Edward M. Marcotte (PLoS Comput. Biol., 2023)

Molecular complex detection in protein interaction networks through reinforcement learning. - Meghana V. Palukuri; Ridhi S. Patil; Edward M. Marcotte (BMC Bioinform., 2023)

Estimating error rates for single molecule protein sequencing experiments. - Matthew Beauregard Smith; Kent Vandervelden; Thomas Blom; Heather D. Stout; James H. Mapes; Tucker M. Folsom; Christopher Martin 011; Angela M. Bardo; Edward M. Marcotte (PLoS Comput. Biol., 2024)