Edward M. Marcotte

35 papers Journal 31Unranked 3

Year	Rank	Type	Title / Venue / Authors
2024	J	`jnl`	Estimating error rates for single molecule protein sequencing experiments. PLoS Comput. Biol. Matthew Beauregard Smith, Kent Vandervelden, Thomas Blom, Heather D. Stout, James H. Mapes, Tucker M. Folsom, Christopher Martin, Angela M. Bardo, Edward M. Marcotte
2023	J	`jnl`	Amino acid sequence assignment from single molecule peptide sequencing data using a two-stage classifier. PLoS Comput. Biol. Matthew Beauregard Smith, Zack Booth Simpson, Edward M. Marcotte
2023	J	`jnl`	Mining Patents with Large Language Models Demonstrates Congruence of Functional Labels and Chemical Structures. CoRR Clayton W. Kosonocky, Claus O. Wilke, Edward M. Marcotte, Andrew D. Ellington
2023	J	`jnl`	Molecular complex detection in protein interaction networks through reinforcement learning. BMC Bioinform. Meghana V. Palukuri, Ridhi S. Patil, Edward M. Marcotte
2022	J	`jnl`	HumanNet v3: an improved database of human gene networks for disease research. Nucleic Acids Res. Chan Yeong Kim, Seungbyn Baek, Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, G. Traver Hart, Insuk Lee
2020	J	`jnl`	Structural Biology in the Multi-Omics Era. J. Chem. Inf. Model. Caitlyn L. McCafferty, Eric J. Verbeke, Edward M. Marcotte, David W. Taylor
2019	J	`jnl`	Ancestral reconstruction of protein interaction networks. PLoS Comput. Biol. Benjamin J. Liebeskind, Richard W. Aldrich, Edward M. Marcotte
2019	J	`jnl`	HumanNet v2: human gene networks for disease research. Nucleic Acids Res. Sohyun Hwang, Chan Yeong Kim, Sunmo Yang, Eiru Kim, G. Traver Hart, Edward M. Marcotte, Insuk Lee
2017	J	`jnl`	GWAB: a web server for the network-based boosting of human genome-wide association data. Nucleic Acids Res. Jung Eun Shim, Changbae Bang, Sunmo Yang, Tak Lee, Sohyun Hwang, Chan Yeong Kim, Ulf Martin Singh-Blom, Edward M. Marcotte, Insuk Lee
2017	J	`jnl`	Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets. PLoS Comput. Biol. Kevin Drew, Christian L. Müller, Richard Bonneau, Edward M. Marcotte
2016	J	`jnl`	Computational discovery of pathway-level genetic vulnerabilities in non-small-cell lung cancer. Bioinform. Jonathan H. Young, Michael Peyton, Hyun Seok Kim, Elizabeth McMillan, John D. Minna, Michael A. White, Edward M. Marcotte
2016	J	`jnl`	MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates. Nucleic Acids Res. Eiru Kim, Sohyun Hwang, Hyojin Kim, Hongseok Shim, Byunghee Kang, Sunmo Yang, Jae Ho Shim, Seung Yeon Shin, Edward M. Marcotte, Insuk Lee
2015	J	`jnl`	A Theoretical Justification for Single Molecule Peptide Sequencing. PLoS Comput. Biol. Jagannath Swaminathan, Alexander A. Boulgakov, Edward M. Marcotte
2015	J	`jnl`	Controlled Measurement and Comparative Analysis of Cellular Components in PLoS Comput. Biol. 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, Jeffrey E. Barrick, Edward M. Marcotte, Claus O. Wilke
2014	J	`jnl`	MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network. Nucleic Acids Res. Sohyun Hwang, Eiru Kim, Sunmo Yang, Edward M. Marcotte, Insuk Lee
2013	J	`jnl`	Prediction of gene-phenotype associations in humans, mice, and plants using phenologs. BMC Bioinform. John O. Woods, Ulf Martin Singh-Blom, Jon M. Laurent, Kriston L. McGary, Edward M. Marcotte
2012	—	`ch.`	Label-Free Protein Quantitation Using Weighted Spectral Counting. Quantitative Methods in Proteomics Christine Vogel, Edward M. Marcotte
2011	J	`jnl`	Revisiting the negative example sampling problem for predicting protein-protein interactions. Bioinform. Yungki Park, Edward M. Marcotte
2009	J	`jnl`	Integrating shotgun proteomics and mRNA expression data to improve protein identification. Bioinform. Smriti R. Ramakrishnan, Christine Vogel, John T. Prince, Rong Wang, Zhihua Li, Luiz O. F. Penalva, Margaret Myers, Edward M. Marcotte, Daniel P. Miranker
2009	J	`jnl`	Mining gene functional networks to improve mass-spectrometry-based protein identification. Bioinform. Smriti R. Ramakrishnan, Christine Vogel, Taejoon Kwon, Luiz O. F. Penalva, Edward M. Marcotte, Daniel P. Miranker
2008	J	`jnl`	Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence. PLoS Comput. Biol. Wan Kyu Kim, Edward M. Marcotte
2008	J	`jnl`	The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results. BMC Bioinform. 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
2008	J	`jnl`	mspire: mass spectrometry proteomics in Ruby. Bioinform. John T. Prince, Edward M. Marcotte
2007	J	`jnl`	A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. BMC Bioinform. G. Traver Hart, Insuk Lee, Edward M. Marcotte
2006	J	`jnl`	A fast coarse filtering method for peptide identification by mass spectrometry. Bioinform. Smriti R. Ramakrishnan, Rui Mao, Aleksey A. Nakorchevskiy, John T. Prince, Willard S. Willard, Weijia Xu, Edward M. Marcotte, Daniel P. Miranker
2006	—	`conf`	Integrating Co-occurrence Statistics with Information Extraction for Robust Retrieval of Protein Interactions from Medline. BioNLP@NAACL-HLT Razvan C. Bunescu, Raymond J. Mooney, Arun K. Ramani, Edward M. Marcotte
2005	J	`jnl`	Comparative experiments on learning information extractors for proteins and their interactions. Artif. Intell. Medicine Razvan C. Bunescu, Ruifang Ge, Rohit J. Kate, Edward M. Marcotte, Raymond J. Mooney, Arun K. Ramani, Yuk Wah Wong
2005	J	`jnl`	Protein function prediction using the Protein Link EXplorer (PLEX). Bioinform. Shailesh V. Date, Edward M. Marcotte
2005	—	`conf`	Using Biomedical Literature Mining to Consolidate the Set of Known Human Protein-Protein Interactions. LBLODMBS@IDMB Arun K. Ramani, Razvan C. Bunescu, Raymond J. Mooney, Edward M. Marcotte
2003	J	`jnl`	Diametrical clustering for identifying anti-correlated gene clusters. Bioinform. Inderjit S. Dhillon, Edward M. Marcotte, Usman Roshan
2002	—	`conf`	Predicting Protein Function and Nworks on a Genomewide Scale. Gene Regulations and Metabolism Edward M. Marcotte
2001	J	`jnl`	DIP: The Database of Interacting Proteins: 2001 update. Nucleic Acids Res. Ioannis Xenarios, Esteban Fernandez, Lukasz Salwínski, Xiaoqun Joyce Duan, Michael J. Thompson, Edward M. Marcotte, David Eisenberg
2001	J	`jnl`	Exploiting Big Biology: Integrating Large-scale Biological Data for Function Inference. Briefings Bioinform. Edward M. Marcotte, Shailesh V. Date
2001	J	`jnl`	Mining literature for protein-protein interactions. Bioinform. Edward M. Marcotte, Ioannis Xenarios, David Eisenberg
2000	J	`jnl`	DIP: the Database of Interacting Proteins. Nucleic Acids Res. Ioannis Xenarios, Danny W. Rice, Lukasz Salwínski, Marisa K. Baron, Edward M. Marcotte, David Eisenberg