Trey Ideker

发表

Integrating scientific cultures

Vineet Bafna, Trey Ideker, Thomas Lemberger, 2007, Molecular systems biology.

Cytoscape 2.8: new features for data integration and network visualization

Trey Ideker, Michael E. Smoot, Keiichiro Ono, 2010, Bioinform..

Dapple: Improved Techniques for Finding Spots on DNA Microarrays

Jeremy Buhler, Trey Ideker, David Haynor, 2000 .

Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape

Trey Ideker, Ralf Herwig, Keiichiro Ono, 2010, Bioinform..

Inferring gene ontologies from pairwise similarity data

Vineet Bafna, Trey Ideker, Michael Yu, 2014, Bioinform..

An Ontology of Functions and Processes Derived from Molecular Networks

Trey Ideker, 2014 .

Session Introduction

Trey Ideker, Vincent Schächter, Erik K. Neumann, 2004, Pacific Symposium on Biocomputing.

Building with a scaffold: emerging strategies for high- to low-level cellular modeling.

Trey Ideker, Douglas Lauffenburger, D. Lauffenburger, 2003, Trends in biotechnology.

A Blueprint for Systems Biology.

Trey Ideker, Leroy Hood, L. Hood, 2019, Clinical chemistry.

Bioinformatics in the human interactome project

Alfonso Valencia, Trey Ideker, 2006, Bioinform..

Physical Network Models

Tommi S. Jaakkola, Trey Ideker, Chen-Hsiang Yeang, 2004, J. Comput. Biol..

VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data

Trey Ideker, Shankar Subramaniam, Albert Hsiao, 2005, Nucleic Acids Res..

NDEx, the Network Data Exchange.

Jing Chen, Trey Ideker, Aleksandar Stojmirovic, 2015, Cell systems.

PathBLAST: a tool for alignment of protein interaction networks

Roded Sharan, Trey Ideker, Brian P. Kelley, 2004, Nucleic Acids Res..

A direct comparison of protein interaction confidence assignment schemes

Roded Sharan, Eytan Ruppin, Trey Ideker, 2006, BMC Bioinformatics.

Protein Networks as Logic Functions in Development and Cancer

Trey Ideker, Janusz Dutkowski, T. Ideker, 2011, PLoS Comput. Biol..

Classifying tumors by supervised network propagation

Wei Zhang, Trey Ideker, Jianzhu Ma, 2018, Bioinform..

Additional data file 5

Farshad Fotouhi, Trey Ideker, Julie A. Hines, 2003 .

Network propagation in the cytoscape cyberinfrastructure

Trey Ideker, Barry Demchak, Dexter Pratt, 2017, PLoS Comput. Biol..

Integrated Assessment and Prediction of Transcription Factor Binding

Trey Ideker, Christopher T. Workman, Ulrich Möller, 2006, PLoS Comput. Biol..

Erratum Bioengineering and Systems Biology

Douglas A. Lauffenburger, Trey Ideker, L. Raimond Winslow, 2006 .

Visualization and Analysis of Biological Networks and Models

Trey Ideker, 2015 .

Offset correction techniques for imaging sensors using random dither information

Trey Ideker, 1995 .

Deep functional synthesis: a machine learning approach to gene functional enrichment

Sheng Wang, Jianzhu Ma, Trey Ideker, 2019, bioRxiv.

Rare variant phasing using paired tumor:normal sequence data

Trey Ideker, Nicholas J. Schork, Hannah Carter, 2019, BMC Bioinformatics.

Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells.

Jianzhu Ma, Trey Ideker, Brent M Kuenzi, 2020, Cancer cell.

Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes

Trey Ideker, Franco Maria Montevecchi, Carlo Vittorio Cannistraci, 2010, Bioinform..

Discovering regulatory and signalling circuits in molecular interaction networks

Benno Schwikowski, Trey Ideker, Andrew F. Siegel, 2002, ISMB.

NeXO Web: the NeXO ontology database and visualization platform

Trey Ideker, Keiichiro Ono, Michael Yu, 2013, Nucleic Acids Res..

Comparison of Protein-Protein Interaction Confidence Assignment Schemes

Roded Sharan, Eytan Ruppin, Trey Ideker, 2005, Systems Biology and Regulatory Genomics.

Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks

Roded Sharan, Richard M. Karp, Trey Ideker, 2005, RECOMB.

Mapping cell structure across scales by fusing protein images and interactions

Jianzhu Ma, Trey Ideker, Wei Ouyang, 2020, bioRxiv.

Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data

Trey Ideker, Nevan J. Krogan, Sourav Bandyopadhyay, 2008, PLoS Comput. Biol..

On entropy and information in gene interaction networks

Trey Ideker, Sara Brin Rosenthal, Kathleen M. Fisch, 2018, Bioinform..

Inferring Pathway Activity toward Precise Disease Classification

Doheon Lee, Trey Ideker, Eunjung Lee, 2008, PLoS Comput. Biol..

Systems Biology and Regulatory Genomics: Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics, San Diego, CA, USA, ... Papers (Lecture Notes in Computer Science)

Benjamin J. Raphael, Trey Ideker, Christopher T. Workman, 2007 .

Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks

Roded Sharan, Richard M. Karp, Trey Ideker, 2006, J. Comput. Biol..

Classifying tumors by supervised network propagation

Trey Ideker, Jianzhu Ma, Wei Zhang, 2018, Bioinform..

ISMB 2008 Organization

Burkhard Rost, Anna Tramontano, Alfonso Valencia, 2008, ISMB.

Visualization and Integration of Protein-Protein Interactions

Benno Schwikowski, Peter Uetz, Trey Ideker, 2001 .

A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression

Helga Thorvaldsdóttir, Trey Ideker, Jill Mesirov, 2017, F1000Research.

Abstract 1317: Multi-scale mapping of the physical and functional architecture of the cancer cell

Trey Ideker, Nevan J. Krogan, Minkyu Kim, 2018 .

Using deep learning to model the hierarchical structure and function of a cell

Roded Sharan, Jianzhu Ma, Trey Ideker, 2018, Nature Methods.

Papers on normalization, variable selection, classification or clustering of microarray data

Joaquín Dopazo, Trey Ideker, Olga G. Troyanskaya, 2009, Bioinform..

Data collection and analysis in systems biology

Trey Ideker, T. Ideker, 2004 .

NetworkBLAST: comparative analysis of protein networks

Roded Sharan, Trey Ideker, Maxim Kalaev, 2008 .

Thousands of missing variants in the UK Biobank are recoverable by genome realignment

Trey Ideker, Tongqiu Jia, Brenton Munson, 2020, Annals of human genetics.

Multiscale community detection in Cytoscape

Trey Ideker, Christopher Churas, Santo Fortunato, 2020, PLoS Comput. Biol..

Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data

Roded Sharan, Richard M. Karp, Ron Shamir, 2004, J. Comput. Biol..

Abstract PHB03: A hierarchical model of DNA repair inferred from omics-scale genetic interaction data reveals the dynamics of DNA damage induction

Trey Ideker, Nevan J. Krogan, Anton Kratz, 2020 .

Discovering Regulated Networks During HIV-1 Latency and Reactivation

Trey Ideker, Sourav Bandyopadhyay, Ryan M. Kelley, 2005, Pacific Symposium on Biocomputing.

Systematic Evaluation of Molecular Networks for Discovery of Disease Genes.

Wei Zhang, Trey Ideker, Pablo Tamayo, 2018, Cell systems.

PiNGO: a Cytoscape plugin to find candidate genes in biological networks

Trey Ideker, Michael E. Smoot, Keiichiro Ono, 2011, Bioinform..

Systems Biology and Computational Proteomics, Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics, San Diego, CA, USA, December 1-3, 2006, Revised Selected Papers

Trey Ideker, Vineet Bafna, on Regulatory Genomics, 2007, Systems Biology and Computational Proteomics.

Network approaches and applications in biology

Ruth Nussinov, Trey Ideker, R. Nussinov, 2017, PLoS Comput. Biol..

Abstract 1310: Systematic evaluation of gene networks for discovery of disease genes

Trey Ideker, Pablo Tamayo, Daniel E. Carlin, 2018 .

The Hallmarks of Cancer Revisited Through Systems Biology and Network Modelling

Charles Auffray, Trey Ideker, Leroy Hood, 2011 .

ndexr—an R package to interface with the network data exchange

Florian Auer, Trey Ideker, Frank Kramer, 2018, Bioinform..

enoLOGOS: a versatile web tool for energy normalized sequence logos

Gary D. Stormo, Trey Ideker, Christopher T. Workman, 2005, Nucleic Acids Res..

pyNBS: a Python implementation for network-based stratification of tumor mutations

Trey Ideker, Daniel E. Carlin, Tongqiu Jia, 2018, Bioinform..

Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls.

Trey Ideker, John Paul Shen, T. Ideker, 2018, Journal of molecular biology.

Abstract PL02-04: Decoding patient genomes through the hierarchical pathway architecture of the cancer cell

Trey Ideker, 2018 .

Proceedings of the 2005 joint annual satellite conference on Systems biology and regulatory genomics

Benjamin J. Raphael, Trey Ideker, Christopher T. Workman, 2005 .

Building Hierarchical Models of the Cell from Genomics Data

Trey Ideker, 2017 .

A census of pathway maps in cancer systems biology

Trey Ideker, Brent M. Kuenzi, T. Ideker, 2020, Nature Reviews Cancer.

Testing for Differentially-Expressed Genes by Maximum-Likelihood Analysis of Microarray Data

Trey Ideker, Vesteinn Thorsson, Leroy E. Hood, 2000, J. Comput. Biol..

DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies.

Jianzhu Ma, Jing Chen, Trey Ideker, 2019, Cell systems.

Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data

Roded Sharan, Richard M. Karp, Ron Shamir, 2005, J. Comput. Biol..

Development of a systems approach for the analysis of toxicogenomic data

Trey Ideker, Christopher T. Workman, Yeyejide Adeleye, 2007 .

Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood

Trey Ideker, Ryan M. Kelley, Hoda Feizi, 2008, Bioinform..

Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

James T. Robinson, Jill P. Mesirov, Anton Nekrutenko, 2015, Nature Methods.

CellCircuits: a database of protein network models

Trey Ideker, Mike Daly, H. Craig Mak, 2006, Nucleic Acids Res..

PROTEIN NETWORK COMPARATIVE GENOMICS

Trey Ideker, 2006 .

Proceedings of the joint 2006 satellite conference on Systems biology and computational proteomics

Vineet Bafna, Trey Ideker, 2006 .

SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments

Roded Sharan, Eytan Ruppin, Trey Ideker, 2007, ISMB/ECCB.

Erratum: Bioengineering and systems biology (Annals of Biomedical Engigeering (2006) DOI: 10.1007/s10439-005-9047-7)

Douglas A. Lauffenburger, Trey Ideker, Douglas A. Lauffenburger, 2006 .

A Fast and Flexible Framework for Network-Assisted Genomic Association

Trey Ideker, Daniel E. Carlin, Samson H. Fong, 2019, iScience.

Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients

Roded Sharan, Jian Peng, Marc Hafner, 2021, Nature Cancer.

Genetic dissection of complex traits using hierarchical biological knowledge

Trey Ideker, Jason F Kreisberg, Hidenori Tanaka, 2021, PLoS Comput. Biol..

Abstract IA-09: Mapping cell structure across scales by fusing protein images and interactions

Trey Ideker, 2021 .

Using Functional Signature Ontology (FUSION) to Identify Mechanisms of Action for Natural Products

Trey Ideker, Yang Xie, Guanghua Xiao, 2013, Science Signaling.

Hot spots for modulating toxicity identified by genomic phenotyping and localization mapping.

Trey Ideker, T. Ideker, L. Samson, 2004, Molecular cell.

Genome-Wide Association Data Reveal a Global Map of Genetic Interactions among Protein Complexes

Richard M. Karp, Trey Ideker, Nevan J. Krogan, 2009, PLoS genetics.

The Cytoscape Automation app article collection

Benno Schwikowski, Gary D Bader, Trey Ideker, 2018, F1000Research.

A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates the B cell fate

Trey Ideker, Janusz Dutkowski, Celso A. Espinoza, 2010, Nature Immunology.

A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy.

Trey Ideker, Justin Huang, Robert W Sobol, 2016, Molecular cell.

Integrating physical and genetic maps: from genomes to interaction networks

Trey Ideker, Andreas Beyer, Sourav Bandyopadhyay, 2007, Nature Reviews Genetics.

The Cytoscape app article collection

Benno Schwikowski, Gary D Bader, Trey Ideker, 2014, F1000Research.

Biomolecular Interaction Networks Cytoscape : A Software Environment for Integrated Models of

Benno Schwikowski, Nada Amin, Trey Ideker, 2003 .

Systems biology guided by XCMS Online metabolomics

Trey Ideker, Royston Goodacre, Tao Huan, 2017, Nature Methods.

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters

Trey Ideker, Barry Demchak, Keiichiro Ono, 2014, F1000Research.

Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy.

Trey Ideker, Rama Balakrishnan, J Michael Cherry, 2017, Molecular cell.

Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus-Host Protein Network.

Trey Ideker, John Von Dollen, Nevan J Krogan, 2018, Cancer discovery.

Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping.

Trey Ideker, Thomas J. Begley, T. Ideker, 2002, Molecular cancer research : MCR.

Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer Types

Trey Ideker, Jason F. Kreisberg, Andrew M. Gross, 2015, PloS one.

Visible Machine Learning for Biomedicine

Benjamin J. Raphael, Trey Ideker, Jianzhu Ma, 2018, Cell.

Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering

Ziv Bar-Joseph, Trey Ideker, Timothy Ravasi, 2010, Genome Biology.

Interactome networks: the state of the science

Trey Ideker, Yeyejide A. Adeleye, Guy J Warner, 2006, Genome Biology.

Differential analysis of high-throughput quantitative genetic interaction data

Trey Ideker, T. Ideker, Gordon J. Bean, 2012, Genome Biology.

Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment

Peter D. Adams, Trey Ideker, Hannah Carter, 2017, Genome Biology.

Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA.

Trey Ideker, Kang Zhang, Daniel Chen, 2016, Molecular cell.

Annotating gene sets by mining large literature collections with protein networks

Jiawei Han, Trey Ideker, Jianzhu Ma, 2017, PSB.

Cytoscape: the network visualization tool for GenomeSpace workflows

Trey Ideker, Ted Liefeld, Jill P Mesirov, 2014, F1000Research.

Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss

Ryan K. Orosco, Trey Ideker, Hannah Carter, 2014, Nature Genetics.

Association of methylation of genes in the taurine/hypotaurine pathway with worse prognosis in renal cell carcinoma.

Trey Ideker, Andrew M. Gross, John Paul Shen, 2013 .

Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal squamous cell carcinoma

Trey Ideker, Michael Considine, Theresa Guo, 2016, International journal of cancer.

DNA Methylation Clocks in Aging: Categories, Causes, and Consequences.

Trey Ideker, Neil A. Robertson, T. Ideker, 2018, Molecular cell.

An Integrated Systems Analysis Implicates EGR1 Downregulation in Simian Immunodeficiency Virus Encephalitis-Induced Neural Dysfunction

Trey Ideker, Timothy Ravasi, Merril Gersten, 2009, The Journal of Neuroscience.

Proteome-wide discovery of mislocated proteins in cancer

Trey Ideker, Han-Yu Chuang, Hyosil Kim, 2013, Genome research.

Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer.

Trey Ideker, Hannah Carter, Christopher M. DeBoever, 2017, Cancer discovery.

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing

Trey Ideker, Claudia Hernandez-Armenta, Brian K. Shoichet, 2020, bioRxiv.

Genotype to phenotype via network analysis.

Trey Ideker, Hannah Carter, T. Ideker, 2013, Current opinion in genetics & development.

Cytoscape: the network visualization tool for GenomeSpace workflows

Trey Ideker, Ted Liefeld, Jill P Mesirov, 2014, F1000Research.

Boosting Signal-to-Noise in Complex Biology: Prior Knowledge Is Power

Trey Ideker, Janusz Dutkowski, Leroy Hood, 2011, Cell.

Quantitative translation of dog-to-human aging by conserved remodeling of epigenetic networks

Peter D. Adams, Trey Ideker, Jianzhu Ma, 2019, bioRxiv.

Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species

Trey Ideker, Andreas Beyer, Han-Yu Chuang, 2008, Nucleic acids research.