Edward M. Marcotte

Publication Activity (10 Years)

Years Active: 2000-2023
Publications (10 Years): 11

Top Topics

Theoretical Justification

Chemical Structures

Top Venues

Nucleic Acids Res.

PLoS Comput. Biol.

Publications

Clayton W. Kosonocky, Claus O. Wilke, Edward M. Marcotte, Andrew D. Ellington
Mining Patents with Large Language Models Demonstrates Congruence of Functional Labels and Chemical Structures. CoRR (2023)
Matthew Beauregard Smith, Zack Booth Simpson, Edward M. Marcotte
Amino acid sequence assignment from single molecule peptide sequencing data using a two-stage classifier. PLoS Comput. Biol. 19 (5) (2023)
Meghana V. Palukuri, Ridhi S. Patil, Edward M. Marcotte
Molecular complex detection in protein interaction networks through reinforcement learning. BMC Bioinform. 24 (1) (2023)
Chan Yeong Kim, Seungbyn Baek, Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, G. Traver Hart, Insuk Lee
HumanNet v3: an improved database of human gene networks for disease research. Nucleic Acids Res. 50 (D1) (2022)
Caitlyn L. McCafferty, Eric J. Verbeke, Edward M. Marcotte, David W. Taylor
Structural Biology in the Multi-Omics Era. J. Chem. Inf. Model. 60 (5) (2020)
Sohyun Hwang, Chan Yeong Kim, Sunmo Yang, Eiru Kim, G. Traver Hart, Edward M. Marcotte, Insuk Lee
HumanNet v2: human gene networks for disease research. Nucleic Acids Res. 47 (Database-Issue) (2019)
Benjamin J. Liebeskind, Richard W. Aldrich, Edward M. Marcotte
Ancestral reconstruction of protein interaction networks. PLoS Comput. Biol. 15 (10) (2019)
Jung Eun Shim, Changbae Bang, Sunmo Yang, Tak Lee, Sohyun Hwang, Chan Yeong Kim, Ulf Martin Singh-Blom, Edward M. Marcotte, Insuk Lee
GWAB: a web server for the network-based boosting of human genome-wide association data. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Kevin Drew, Christian L. Müller, Richard Bonneau, Edward M. Marcotte
Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets. PLoS Comput. Biol. 13 (10) (2017)
Eiru Kim, Sohyun Hwang, Hyojin Kim, Hongseok Shim, Byunghee Kang, Sunmo Yang, Jae Ho Shim, Seung Yeon Shin, Edward M. Marcotte, Insuk Lee
MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates. Nucleic Acids Res. 44 (Database-Issue) (2016)
Jonathan H. Young, Michael Peyton, Hyun Seok Kim, Elizabeth McMillan, John D. Minna, Michael A. White, Edward M. Marcotte
Computational discovery of pathway-level genetic vulnerabilities in non-small-cell lung cancer. Bioinform. 32 (9) (2016)
Jagannath Swaminathan, Alexander A. Boulgakov, Edward M. Marcotte
A Theoretical Justification for Single Molecule Peptide Sequencing. PLoS Comput. Biol. 11 (2) (2015)
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
Reveals Broad Regulatory Changes in Response to Glucose Starvation. PLoS Comput. Biol. 11 (8) (2015)
Sohyun Hwang, Eiru Kim, Sunmo Yang, Edward M. Marcotte, Insuk Lee
MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
John O. Woods, Ulf Martin Singh-Blom, Jon M. Laurent, Kriston L. McGary, Edward M. Marcotte
Prediction of gene-phenotype associations in humans, mice, and plants using phenologs. BMC Bioinform. 14 (2013)
Yungki Park, Edward M. Marcotte
Revisiting the negative example sampling problem for predicting protein-protein interactions. Bioinform. 27 (21) (2011)
Smriti R. Ramakrishnan, Christine Vogel, John T. Prince, Rong Wang, Zhihua Li, Luiz O. F. Penalva, Margaret Myers, Edward M. Marcotte, Daniel P. Miranker
Integrating shotgun proteomics and mRNA expression data to improve protein identification. Bioinform. 25 (11) (2009)
Smriti R. Ramakrishnan, Christine Vogel, Taejoon Kwon, Luiz O. F. Penalva, Edward M. Marcotte, Daniel P. Miranker
Mining gene functional networks to improve mass-spectrometry-based protein identification. Bioinform. 25 (22) (2009)
Wan Kyu Kim, Edward M. Marcotte
Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence. PLoS Comput. Biol. 4 (11) (2008)
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
The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results. BMC Bioinform. 9 (2008)
John T. Prince, Edward M. Marcotte
mspire: mass spectrometry proteomics in Ruby. Bioinform. 24 (23) (2008)
G. Traver Hart, Insuk Lee, Edward M. Marcotte
A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. BMC Bioinform. 8 (2007)
Razvan C. Bunescu, Raymond J. Mooney, Arun K. Ramani, Edward M. Marcotte
Integrating Co-occurrence Statistics with Information Extraction for Robust Retrieval of Protein Interactions from Medline. BioNLP@NAACL-HLT (2006)
Smriti R. Ramakrishnan, Rui Mao, Aleksey A. Nakorchevskiy, John T. Prince, Willard S. Willard, Weijia Xu, Edward M. Marcotte, Daniel P. Miranker
A fast coarse filtering method for peptide identification by mass spectrometry. Bioinform. 22 (12) (2006)
Shailesh V. Date, Edward M. Marcotte
Protein function prediction using the Protein Link EXplorer (PLEX). Bioinform. 21 (10) (2005)
Arun K. Ramani, Razvan C. Bunescu, Raymond J. Mooney, Edward M. Marcotte
Using Biomedical Literature Mining to Consolidate the Set of Known Human Protein-Protein Interactions. LBLODMBS@IDMB (2005)
Razvan C. Bunescu, Ruifang Ge, Rohit J. Kate, Edward M. Marcotte, Raymond J. Mooney, Arun K. Ramani, Yuk Wah Wong
Comparative experiments on learning information extractors for proteins and their interactions. Artif. Intell. Medicine 33 (2) (2005)
Inderjit S. Dhillon, Edward M. Marcotte, Usman Roshan
Diametrical clustering for identifying anti-correlated gene clusters. Bioinform. 19 (13) (2003)
Edward M. Marcotte
Predicting Protein Function and Nworks on a Genomewide Scale. Gene Regulations and Metabolism (2002)
Edward M. Marcotte, Ioannis Xenarios, David S. Eisenberg
Mining literature for protein-protein interactions. Bioinform. 17 (4) (2001)
Ioannis Xenarios, Esteban Fernandez, Lukasz Salwínski, Xiaoqun Joyce Duan, Michael J. Thompson, Edward M. Marcotte, David S. Eisenberg
DIP: The Database of Interacting Proteins: 2001 update. Nucleic Acids Res. 29 (1) (2001)
Edward M. Marcotte, Shailesh V. Date
Exploiting Big Biology: Integrating Large-scale Biological Data for Function Inference. Briefings Bioinform. 2 (4) (2001)
Ioannis Xenarios, Danny W. Rice, Lukasz Salwínski, Marisa K. Baron, Edward M. Marcotte, David S. Eisenberg
DIP: the Database of Interacting Proteins. Nucleic Acids Res. 28 (1) (2000)