Gary D. Bader

发表

Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic

Gary D. Bader, Gary D Bader, Ryan Sun, 2018, bioRxiv.

Erratum: The BioPAX community standard for pathway data sharing (Nat. Biotechnol. (2010) 28 (935-942)

Gary D. Bader, Frank Schacherer, Edgar Wingender, 2010 .

Abstract 1284: How can you interpret gene lists from -omics experiments

Gary D. Bader, Chris Sander, Gary D Bader, 2018, Bioinformatics and Systems Biology.

GeneMANIA Prediction Server 2013 Update

Gary D. Bader, Gary D Bader, Quaid Morris, 2013, Nucleic Acids Res..

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

Gary D. Bader, George Wright, Gary D Bader, 2010, Nucleic Acids Res..

GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop

Gary D. Bader, George Wright, Gary D Bader, 2010, Bioinform..

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017

Gary D. Bader, Chris J. Myers, Gary D Bader, 2018, J. Integr. Bioinform..

netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks

Gary D. Bader, Shraddha Pai, Gary D Bader, 2020, F1000Research.

A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain–peptide interaction from primary sequence

Gary D. Bader, Gary D Bader, Naiyang Deng, 2010, Bioinform..

DeCLUTR: Deep Contrastive Learning for Unsupervised Textual Representations pdf

Gary D. Bader, Gary D Bader, Bo Wang, 2020, ACL.

cPath: open source software for collecting, storing, and querying biological pathways

Gary D. Bader, Chris Sander, Gary D Bader, 2006, BMC Bioinformatics.

Mapping genetic interactions in various contexts provides complementary information

Gary D. Bader, Gary D Bader, Magali Michaut, 2011 .

Evaluation of methods to assign cell type labels to cell clusters from single-cell RNAsequencing data

Gary D. Bader, John H. Morris, Alexander R. Pico, 2019 .

The Biomolecular Interaction Network Database in PSI-MI 2.5

Gary D. Bader, Gary D Bader, Rashad Badrawi, 2011, Database J. Biol. Databases Curation.

The BioPAX Validator

Gary D. Bader, Chris Sander, Emek Demir, 2013, Bioinform..

miRScape: A Cytoscape Plugin to Annotate Biological Networks with microRNAs

Gary D. Bader, Dennis Shasha, Gary D Bader, 2009 .

Specifications of Standards in Systems and Synthetic Biology

Gary D. Bader, Chris J. Myers, Gary D Bader, 2015, J. Integr. Bioinform..

Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative

Gary D. Bader, Chris J. Myers, Gary D Bader, 2015, Front. Bioeng. Biotechnol..

SeqHound: biological sequence and structure database as a platform for bioinformatics research

Gary D. Bader, Katerina Michalickova, Christopher W. V. Hogue, 2002, BMC Bioinformatics.

Protein Complexes are Central in the Yeast Genetic Landscape

Gary D. Bader, Gary D Bader, Michael Costanzo, 2011, PLoS Comput. Biol..

Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction

Gary D. Bader, Gary D Bader, Quaid Morris, 2014, Front. Genet..

Cytoscape ESP: simple search of complex biological networks

Allan Kuchinsky, Gary D. Bader, Gary D Bader, 2008, Bioinform..

Faculty Opinions recommendation of Measuring the evolutionary rewiring of biological networks.

Gary D. Bader, Gary D Bader, Magali Michaut, 2011 .

Cytoscape.js: a graph theory library for visualisation and analysis

Gary D. Bader, Gary D Bader, Yue Dong, 2015, Bioinform..

Predicting physiologically relevant SH3 domain mediated protein–protein interactions in yeast

Gary D. Bader, Gary D Bader, Shobhit Jain, 2016, Bioinform..

SyQUAL: a platform for qualitative modelling and simulation of biological systems

Gary D. Bader, Gary D Bader, Franco Fummi, 2016, 2016 IEEE International High Level Design Validation and Test Workshop (HLDVT).

Pathway Commons, a web resource for biological pathway data

Gary D. Bader, Chris Sander, Gary D Bader, 2010, Nucleic Acids Res..

WordCloud: a Cytoscape plugin to create a visual semantic summary of networks

Gary D. Bader, Gary D Bader, Daniele Merico, 2011, Source Code for Biology and Medicine.

GeneMANIA update 2018

Gary D. Bader, Gary D Bader, Quaid Morris, 2018, Nucleic Acids Res..

NetMatchStar: an enhanced Cytoscape network querying app (version 1; referees: 2 approved)

Gary D. Bader, Dennis Shasha, Gary D Bader, 2015 .

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

Jun Yu, Chen Hong, Ken Chen, 2020, Nature.

Global neuroscience and mental health research: a bibliometrics case study

Gary D. Bader, Ruth Isserlin, Alison Buchan, 2016, Scientometrics.

A brief history of COMBINE

Gary D. Bader, Chris J. Myers, Gary D Bader, 2017, 2017 Winter Simulation Conference (WSC).

Dataset Descriptions: HCLS Community Profile

Gary D. Bader, Michel Dumontier, Alasdair J. G. Gray, 2015 .

Intelligent worm gene function prediction with GeneMANIA

Gary D. Bader, Gary D Bader, Sylva L. Donaldson, 2010 .

How can you interpret gene lists from -omics experiments?

Gary D. Bader, Chris Sander, Gary D Bader, 2017 .

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019

Gary D. Bader, Chris J. Myers, Gary D Bader, 2019, J. Integr. Bioinform..

An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology

Gary D. Bader, Gary D Bader, Shobhit Jain, 2010, BMC Bioinformatics.

DRYGIN: a database of quantitative genetic interaction networks in yeast

Gary D. Bader, Gary D Bader, Judice L. Y. Koh, 2009, Nucleic Acids Res..

BIND-a data specification for storing and describing biomolecular interactions, molecular complexes and pathways

Gary D. Bader, Christopher W. V. Hogue, Gary D Bader, 2000, Bioinform..

Towards reliable named entity recognition in the biomedical domain

Gary D. Bader, Gary D Bader, John M Giorgi, 2019, bioRxiv.

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016

Gary D. Bader, Chris J. Myers, Gary D Bader, 2016, J. Integr. Bioinform..

Transfer learning for biomedical named entity recognition with neural networks

Gary D. Bader, Gary D Bader, John M. Giorgi, 2018, bioRxiv.

Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study

Gary D. Bader, Reda Alhajj, Gary D Bader, 2012, BMC Systems Biology.

Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data

Gary D. Bader, Gary D Bader, Thinh N Tran, 2019, bioRxiv.

Proteome scanning to predict PDZ domain interactions using support vector machines

Gary D. Bader, Gary D Bader, Shirley Hui, 2010, BMC Bioinformatics.

Ten Simple Rules for Developing Public Biological Databases

Gary D. Bader, Gary D Bader, Mohamed Helmy, 2016, PLoS Comput. Biol..

NetMatchStar : an enhanced Cytoscape network querying app

Gary D. Bader, Gary D Bader, Dennis Shasha, 2017 .

BIND: the Biomolecular Interaction Network Database

Ian M. Donaldson, Cheryl Wolting, Gary D. Bader, 2001, Nucleic Acids Res..

GeStoDifferent: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process

Gary D. Bader, Giancarlo Mauri, Giulio Caravagna, 2013, Bioinform..

Inferring interaction type in gene regulatory networks using co-expression data

Gary D. Bader, Gary D Bader, Mehdi Sadeghi, 2015, Algorithms for Molecular Biology.

BIND: THE BIOMOLECULAR INTERACTION DATABASE

Ian M. Donaldson, Cheryl Wolting, Gary D. Bader, 2001 .

A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway

Gary D. Bader, Gary D Bader, Akhilesh Pandey, 2011, Database J. Biol. Databases Curation.

clusterMaker: a multi-algorithm clustering plugin for Cytoscape

Gary D. Bader, Gang Su, Gary D Bader, 2011, BMC Bioinformatics.

Predicting PDZ domain mediated protein interactions from structure

Gary D. Bader, Gary D Bader, Xiang Xing, 2013, BMC Bioinformatics.

Using Biological Pathway Data with Paxtools

Gary D. Bader, Chris Sander, Gary D Bader, 2013, PLoS Comput. Biol..

A reference map of the human binary protein interactome

Patrick Aloy, Gary D. Bader, Yang Wang, 2020, Nature.

NetSlim: high-confidence curated signaling maps

Gary D. Bader, Gary D Bader, Akhilesh Pandey, 2011, Database J. Biol. Databases Curation.

Cytoscape App Store

Gary D. Bader, Gary D Bader, Yue Dong, 2013, Bioinform..

BioPAX - Biological Pathways Exchange Language Level 2, Version 1.0 Documentation

Gary D. Bader, Christopher W. V. Hogue, Edgar Wingender, 2005 .

BioPAX – biological pathway data exchange format

Gary D. Bader, Chris Sander, Gary D Bader, 2006 .

Erratum to: Inferring interaction type in gene regulatory networks using co-expression data

Gary D. Bader, Mehdi Sadeghi, Pegah Khosravi, 2015, Algorithms Mol. Biol..

SIREN Cytoscape plugin: Interaction Type Discrimination in Gene Regulatory Networks

Gary D. Bader, Gary D Bader, Pegah Khosravi, 2015, 1512.05067.

Faculty Opinions recommendation of STITCH: interaction networks of chemicals and proteins.

Gary D. Bader, Gary D Bader, Iain M. Wallace, 2010 .

SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks

Gary D. Bader, Gary D Bader, Michael L. Blinov, 2020, bioRxiv.

HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery

Gary D. Bader, Gary D Bader, Jüri Reimand, 2014, Bioinform..

netDx: Interpretable patient classification using integrated patient similarity networks

Gary D. Bader, Shraddha Pai, Shirley Hui, 2016, bioRxiv.

Pathguide: a Pathway Resource List

Gary D. Bader, Chris Sander, Gary D Bader, 2005, Nucleic Acids Res..

End-to-end Named Entity Recognition and Relation Extraction using Pre-trained Language Models pdf

Gary D. Bader, Gary D Bader, Bo Wang, 2019, ArXiv.

The Cytoscape Automation app article collection [version 1; referees: Not peer reviewed]

Gary D. Bader, Benno Schwikowski, John H. Morris, 2018 .

IntOGen - TCGA pan-cancer12 high confidence drivers

Gary D. Bader, Gary D Bader, Gad Getz, 2013 .

An automated method for finding molecular complexes in large protein interaction networks

Gary D. Bader, Christopher W. V. Hogue, Gary D Bader, 2003, BMC Bioinformatics.

Enrichment Map – a Cytoscape app to visualize and explore OMICs pathway enrichment results

Gary D. Bader, Gary D Bader, Daniele Merico, 2014, F1000Research.

netDx: Building an interpretable patient classifier with multi-omic data integration andpatient similarity networks

Gary D. Bader, Shraddha Pai, Gary D Bader, 2020 .

Transfer learning for biomedical named entity recognition with neural networks

Gary D. Bader, John M Giorgi, 2018 .

Pathway Commons: 2019 Update

Gary D. Bader, Gary D Bader, Ugur Dogrusoz, 2019, bioRxiv.

Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli

Gary D. Bader, Gary D Bader, Ashkan Golshani, 2015, Bioinform..

Cytoscape Web: an interactive web-based network browser

Gary D. Bader, Gary D Bader, Sylva L. Donaldson, 2010, Bioinform..

Multiple Genetic Interaction Experiments Provide Complementary Information Useful for Gene Function Prediction

Gary D. Bader, Gary D Bader, Magali Michaut, 2012, PLoS Comput. Biol..

Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing.

Gary D. Bader, Gary D Bader, Somasekar Seshagiri, 2010, Molecular bioSystems.

AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations

Gary D. Bader, Gary D Bader, Harm Nijveen, 2016, F1000Research.

Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins

Gary D. Bader, Gary D Bader, Somasekar Seshagiri, 2009, PLoS biology.

Single-cell transcriptomic profiling of the aging mouse brain

Gary D. Bader, Gary D Bader, Aviv Regev, 2019, Nature Neuroscience.

A network analysis to identify mediators of germline-driven differences in breast cancer prognosis

Gary D. Bader, Christine L. Clarke, Gary D Bader, 2020, Nature Communications.

Germ-line DNA copy number variation frequencies in a large North American population

Gary D. Bader, Steven Gallinger, Gary D Bader, 2007, Human Genetics.

The mutational landscape of phosphorylation signaling in cancer

Gary D. Bader, Gary D Bader, Omar Wagih, 2013, Scientific Reports.

MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets

Gary D. Bader, Gary D Bader, TaeHyung Kim, 2011, Nucleic acids research.

Divergent clonal selection dominates medulloblastoma at recurrence

Gary D. Bader, Steven J. M. Jones, Gary D Bader, 2016, Nature.

The BioPAX community standard for pathway data sharing (Nature Biotechnology (2010) 28, (935-942))

Kei-Hoi Cheung, Gary D. Bader, Frank Schacherer, 2012 .

Metabolic Adaptation to Chronic Inhibition of Mitochondrial Protein Synthesis in Acute Myeloid Leukemia Cells

Gary D. Bader, Gary D Bader, Mahadeo A. Sukhai, 2013, PloS one.

Integrative pharmacogenomics to infer large-scale drug taxonomy

Laleh Soltan Ghoraie, Gary D. Bader, Gary D Bader, 2016, bioRxiv.

Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer

Gary D. Bader, Gary D Bader, Jüri Reimand, 2016, Genome Medicine.

Mapping the Cellular Response to Small Molecules Using Chemogenomic Fitness Signatures

Gary D. Bader, Gary D Bader, Sundari Suresh, 2014, Science.

A reference map of the human protein interactome

Gary D. Bader, Yang Wang, Gary D Bader, 2019, bioRxiv.