Trey Ideker
#23,026
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Trey Ideker's AcademicInfluence.com Rankings
Trey Idekerbiology Degrees
Biology
#992
World Rank
#1719
Historical Rank
#527
USA Rank
Genetics
#291
World Rank
#344
Historical Rank
#134
USA Rank
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Biology
Trey Ideker's Degrees
- PhD Bioengineering University of California, San Diego
- Bachelors Bioengineering University of California, San Diego
Why Is Trey Ideker Influential?
(Suggest an Edit or Addition)According to Wikipedia, Trey Ideker is a professor of medicine and bioengineering at UC San Diego. He is the Director of the National Resource for Network Biology, the San Diego Center for Systems Biology, and the Cancer Cell Map Initiative. He uses genome-scale measurements to construct network models of cellular processes and disease.
Trey Ideker's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Cytoscape: a software environment for integrated models of biomolecular interaction networks. (2003) (31344)
- Cytoscape 2.8: new features for data integration and network visualization (2010) (4273)
- A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing (2020) (3012)
- Integration of biological networks and gene expression data using Cytoscape (2007) (2342)
- Genome-wide methylation profiles reveal quantitative views of human aging rates. (2013) (2254)
- Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. (2001) (2037)
- Integrated Genomic Characterization of Papillary Thyroid Carcinoma (2014) (2007)
- A new approach to decoding life: systems biology. (2001) (1750)
- Network-based classification of breast cancer metastasis (2007) (1491)
- A travel guide to Cytoscape plugins (2012) (1255)
- Discovering regulatory and signalling circuits in molecular interaction networks (2002) (1211)
- Global Analysis of Host-Pathogen Interactions that Regulate Early-Stage HIV-1 Replication (2008) (995)
- Conserved patterns of protein interaction in multiple species. (2005) (857)
- Human Host Factors Required for Influenza Virus Replication (2010) (825)
- Protein networks in disease. (2008) (798)
- Differential network biology (2012) (716)
- Complementary Profiling of Gene Expression at the Transcriptome and Proteome Levels in Saccharomyces cerevisiae*S (2002) (657)
- Network-based stratification of tumor mutations (2013) (646)
- An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man (2010) (592)
- Conserved pathways within bacteria and yeast as revealed by global protein network alignment (2003) (558)
- Modeling cellular machinery through biological network comparison (2006) (556)
- Integrative approaches for finding modular structure in biological networks (2013) (507)
- Functional genomic screen for modulators of ciliogenesis and cilium length (2010) (493)
- Inferring Pathway Activity toward Precise Disease Classification (2008) (488)
- A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates the B cell fate (2010) (482)
- Systematic interpretation of genetic interactions using protein networks (2005) (469)
- Host Cell Factors in HIV Replication: Meta-Analysis of Genome-Wide Studies (2009) (462)
- Rewiring of Genetic Networks in Response to DNA Damage (2010) (458)
- A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing (2020) (456)
- Exome Sequencing Links Corticospinal Motor Neuron Disease to Common Neurodegenerative Disorders (2014) (452)
- Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms (2020) (444)
- Metabolomics reveals signature of mitochondrial dysfunction in diabetic kidney disease. (2013) (429)
- PathBLAST: a tool for alignment of protein interaction networks (2004) (427)
- Network propagation: a universal amplifier of genetic associations (2017) (418)
- DNA methylation aging clocks: challenges and recommendations (2019) (393)
- Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae (2006) (378)
- Conservation and Rewiring of Functional Modules Revealed by an Epistasis Map in Fission Yeast (2008) (356)
- Mining SNPs from EST databases. (1999) (352)
- Testing for Differentially-Expressed Genes by Maximum-Likelihood Analysis of Microarray Data (2000) (340)
- Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis (2013) (332)
- Discovery of regulatory interactions through perturbation: inference and experimental design. (1999) (314)
- DNA Methylation Clocks in Aging: Categories, Causes, and Consequences. (2018) (312)
- A decade of systems biology. (2010) (298)
- Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks (2005) (296)
- A Systems Approach to Mapping DNA Damage Response Pathways (2006) (279)
- Multiple Pathways Are Co-regulated by the Protein Kinase Snf1 and the Transcription Factors Adr1 and Cat8* (2003) (275)
- Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions (2017) (270)
- A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. (2008) (266)
- A proteome-wide protein interaction map for Campylobacter jejuni (2007) (261)
- Leveraging models of cell regulation and GWAS data in integrative network-based association studies (2012) (249)
- Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri (2006) (248)
- Using deep learning to model the hierarchical structure and function of a cell (2018) (242)
- enoLOGOS: a versatile web tool for energy normalized sequence logos (2005) (236)
- MHC-I Genotype Restricts the Oncogenic Mutational Landscape (2017) (229)
- Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data (2004) (217)
- Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment (2017) (217)
- Systematic identification of functional orthologs based on protein network comparison. (2006) (215)
- A Human MAP Kinase Interactome (2010) (212)
- Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA. (2016) (206)
- Building with a scaffold: emerging strategies for high- to low-level cellular modeling. (2003) (203)
- NDEx, the Network Data Exchange. (2015) (202)
- Mitochondria, Energetics, Epigenetics, and Cellular Responses to Stress (2014) (199)
- Hierarchical modularity and the evolution of genetic interactomes across species. (2012) (198)
- Integrating physical and genetic maps: from genomes to interaction networks (2007) (194)
- Integrating phenotypic and expression profiles to map arsenic-response networks (2004) (191)
- Transcriptome profiling to identify genes involved in peroxisome assembly and function (2002) (190)
- A gene ontology inferred from molecular networks (2012) (184)
- Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. (2018) (184)
- Physical Network Models (2004) (181)
- Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping. (2002) (180)
- Boosting Signal-to-Noise in Complex Biology: Prior Knowledge Is Power (2011) (179)
- Evolutionarily Conserved Herpesviral Protein Interaction Networks (2009) (177)
- Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p (2009) (165)
- An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man (2010) (165)
- Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data (2008) (153)
- Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling (2013) (148)
- Phosphorylation of LC3 by the Hippo kinases STK3/STK4 is essential for autophagy. (2015) (145)
- The Plasmodium protein network diverges from those of other eukaryotes (2005) (143)
- Systems biology guided by XCMS Online metabolomics (2017) (140)
- eQED: an efficient method for interpreting eQTL associations using protein networks (2008) (138)
- Dapple: Improved Techniques for Finding Spots on DNA Microarrays (2000) (138)
- A direct comparison of protein interaction confidence assignment schemes (2006) (137)
- Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions (2017) (137)
- Genetic interaction mapping in mammalian cells using CRISPR interference (2017) (132)
- Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells. (2020) (129)
- Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineages in hematopoietic progenitors. (2011) (127)
- A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy. (2016) (125)
- NetworkBLAST: comparative analysis of protein networks (2008) (124)
- Genotype to phenotype via network analysis. (2013) (122)
- SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments (2007) (117)
- Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss (2014) (113)
- Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer. (2017) (108)
- Visible Machine Learning for Biomedicine (2018) (108)
- Validation and refinement of gene-regulatory pathways on a network of physical interactions (2005) (105)
- The cancer cell map initiative: defining the hallmark networks of cancer. (2015) (105)
- Hot spots for modulating toxicity identified by genomic phenotyping and localization mapping. (2004) (104)
- Functional genome-wide siRNA screen identifies KIAA0586 as mutated in Joubert syndrome (2015) (103)
- Protein Networks as Logic Functions in Development and Cancer (2011) (102)
- A global transcriptional network connecting noncoding mutations to changes in tumor gene expression (2018) (101)
- VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data (2005) (100)
- Integrated Assessment and Prediction of Transcription Factor Binding (2006) (99)
- Cost effective strategies for completing the Interactome (2008) (98)
- Dissection of DNA damage responses using multiconditional genetic interaction maps. (2013) (92)
- A Multiscale Map of the Stem Cell State in Pancreatic Adenocarcinoma (2019) (90)
- Rac2 Controls Tumor Growth, Metastasis and M1-M2 Macrophage Differentiation In Vivo (2014) (90)
- Cytoscape: the network visualization tool for GenomeSpace workflows. (2014) (87)
- Cytoscape: the network visualization tool for GenomeSpace workflows (2014) (84)
- High Temperature Requirement Factor A1 (HTRA1) Gene Regulates Angiogenesis through Transforming Growth Factor-β Family Member Growth Differentiation Factor 6* (2011) (84)
- Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes (2010) (80)
- Inferring gene ontologies from pairwise similarity data (2014) (79)
- Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species (2008) (77)
- DNA replication stress differentially regulates G1/S genes via Rad53‐dependent inactivation of Nrm1 (2012) (77)
- Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression. (2011) (74)
- Functional Landscape of SARS-CoV-2 Cellular Restriction (2020) (71)
- PKCε Promotes Oncogenic Functions of ATF2 in the Nucleus while Blocking Its Apoptotic Function at Mitochondria (2012) (70)
- Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis. (2018) (69)
- Coevolution within a transcriptional network by compensatory trans and cis mutations. (2010) (69)
- Genome-Wide Association Data Reveal a Global Map of Genetic Interactions among Protein Complexes (2009) (68)
- Systems biology 101—what you need to know (2004) (68)
- Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems (2016) (68)
- Using Functional Signature Ontology (FUSION) to Identify Mechanisms of Action for Natural Products (2013) (67)
- A systems approach to delineate functions of paralogous transcription factors: Role of the Yap family in the DNA damage response (2008) (63)
- Multivariate analysis of 1.5 million people identifies genetic associations with traits related to self-regulation and addiction (2021) (62)
- Transcriptional regulation of protein complexes within and across species (2007) (62)
- Checkpoint kinases regulate a global network of transcription factors in response to DNA damage. (2013) (61)
- Network propagation in the cytoscape cyberinfrastructure (2017) (61)
- Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus-Host Protein Network. (2018) (60)
- The Dfm1 Derlin Is Required for ERAD Retrotranslocation of Integral Membrane Proteins. (2018) (60)
- Identifying Epistasis in Cancer Genomes: A Delicate Affair (2019) (59)
- Papers on normalization, variable selection, classification or clustering of microarray data (2009) (59)
- De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences (2020) (59)
- Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients (2021) (58)
- Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling. (2015) (57)
- Functional landscape of SARS-CoV-2 cellular restriction (2021) (57)
- Decoupling epigenetic and genetic effects through systematic analysis of gene position. (2013) (56)
- Genome-Wide Fitness and Expression Profiling Implicate Mga2 in Adaptation to Hydrogen Peroxide (2009) (54)
- NDEx 2.0: A Clearinghouse for Research on Cancer Pathways. (2017) (54)
- Leveraging premalignant biology for immune-based cancer prevention (2016) (52)
- Bayesian network analysis of targeting interactions in chromatin. (2010) (52)
- Biomolecular Interaction Networks Cytoscape : A Software Environment for Integrated Models of (2003) (51)
- Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome. (2020) (47)
- Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace (2015) (47)
- Proteome-wide discovery of mislocated proteins in cancer (2013) (46)
- Bioengineering and Systems Biology (2006) (45)
- Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers (2019) (45)
- Global architecture of genetic interactions on the protein network (2003) (45)
- A SARS-CoV-2 protein interaction map reveals targets for drug repurposing (2020) (43)
- Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer. (2013) (42)
- Landscape of protein–protein interactions in Drosophila immune deficiency signaling during bacterial challenge (2013) (41)
- Disruption of NSD1 in Head and Neck Cancer Promotes Favorable Chemotherapeutic Responses Linked to Hypomethylation (2018) (40)
- PiNGO: a Cytoscape plugin to find candidate genes in biological networks (2011) (40)
- A census of pathway maps in cancer systems biology (2020) (39)
- Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal squamous cell carcinoma (2016) (39)
- Cell-autonomous circadian clock of hepatocytes drives rhythms in transcription and polyamine synthesis (2011) (39)
- Understudied proteins: opportunities and challenges for functional proteomics (2022) (38)
- Network approaches and applications in biology (2017) (38)
- Challenges in identifying cancer genes by analysis of exome sequencing data (2016) (38)
- An Integrated Systems Analysis Implicates EGR1 Downregulation in Simian Immunodeficiency Virus Encephalitis-Induced Neural Dysfunction (2009) (37)
- Mapping Plant Interactomes Using Literature Curated and Predicted Protein–Protein Interaction Data Sets[W] (2010) (37)
- Genomic Landscape of Appendiceal Neoplasms. (2018) (35)
- HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers (2020) (35)
- Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering (2010) (35)
- Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer Types (2015) (35)
- A systems approach to discovering signaling and regulatory pathways--or, how to digest large interaction networks into relevant pieces. (2004) (34)
- Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape (2010) (33)
- Cytoscape tools for the web age: D3.js and Cytoscape.js exporters (2014) (32)
- Systems biology analysis reveals role of MDM2 in diabetic nephropathy. (2016) (32)
- Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy. (2017) (30)
- Development of Ultra-High-Density Screening Tools for Microbial “Omics” (2014) (29)
- Matrix-Metalloproteinases in Head and Neck Carcinoma–Cancer Genome Atlas Analysis and Fluorescence Imaging in Mice (2014) (29)
- Classifying tumors by supervised network propagation (2018) (29)
- Dot1 promotes H2B ubiquitination by a methyltransferase-independent mechanism (2018) (28)
- A protein interaction landscape of breast cancer (2021) (28)
- ERCC1 and TS Expression as Prognostic and Predictive Biomarkers in Metastatic Colon Cancer (2015) (28)
- Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls (2016) (28)
- Multiscale community detection in Cytoscape (2020) (27)
- Parenchymal Volumetric Assessment as a Predictive Tool to Determine Renal Function Benefit of Nephron-Sparing Surgery Compared with Radical Nephrectomy. (2016) (27)
- CellCircuits: a database of protein network models (2006) (27)
- Evidence for a common evolutionary rate in metazoan transcriptional networks (2015) (26)
- Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages (2020) (26)
- Assembling global maps of cellular function through integrative analysis of physical and genetic networks (2011) (26)
- A UV-induced genetic network links the RSC complex to nucleotide excision repair and shows dose-dependent rewiring. (2013) (26)
- Unveiling Complexity and Multipotentiality of Early Heart Fields (2021) (26)
- Evolutionary trends and functional anatomy of the human expanded autophagy network (2015) (25)
- Discovering Regulated Networks During HIV-1 Latency and Reactivation (2005) (25)
- Dynamic reprogramming of transcription factors to and from the subtelomere. (2009) (25)
- Siri of the Cell: What Biology Could Learn from the iPhone (2014) (25)
- Transcriptional repression of IFNβ1 by ATF2 confers melanoma resistance to therapy (2015) (24)
- Network-driven plasma proteomics expose molecular changes in the Alzheimer’s brain (2016) (24)
- A multi-scale map of cell structure fusing protein images and interactions (2021) (23)
- Visualization and Integration of Protein-Protein Interactions (2001) (23)
- HiDeF: identifying persistent structures in multiscale ‘omics data (2021) (22)
- A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity (2021) (22)
- Parallel genome-wide screens identify synthetic viable interactions between the BLM helicase complex and Fanconi anemia (2017) (20)
- Quantitative proteomics reveal ATM kinase-dependent exchange in DNA damage response complexes. (2012) (20)
- A Fast and Flexible Framework for Network-Assisted Genomic Association (2019) (19)
- Differential analysis of high-throughput quantitative genetic interaction data (2012) (19)
- Negative selection: a method for obtaining low-abundance cDNAs using high-density cDNA clone arrays. (1999) (19)
- The great hairball gambit (2019) (19)
- pyNBS: a Python implementation for network-based stratification of tumor mutations (2018) (19)
- Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluorescence for Microbial Growth Experiments (2015) (18)
- Typing tumors using pathways selected by somatic evolution (2018) (17)
- Annotating gene sets by mining large literature collections with protein networks (2017) (17)
- Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls. (2018) (17)
- POINT: Are we prepared for the future doctor visit? (2011) (17)
- Combined TP53 mutation/3p loss correlates with decreased radiosensitivity and increased matrix-metalloproteinase activity in head and neck carcinoma. (2015) (17)
- DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies. (2019) (16)
- Thousands of missing variants in the UK BioBank are recoverable by genome realignment (2019) (16)
- Bioinformatics in the human interactome project (2006) (16)
- Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy (2021) (15)
- Integrating scientific cultures (2007) (15)
- An open invitation to the Understudied Proteins Initiative (2022) (15)
- Mapping the protein-protein and genetic interactions of cancer to guide precision medicine. (2019) (14)
- NeXO Web: the NeXO ontology database and visualization platform (2013) (14)
- Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood (2008) (13)
- Bioengineering and Systems Biology (2006) (13)
- Network genomics. (2007) (13)
- Proteome-wide remodeling of protein location and function by stress (2014) (12)
- Molecular networks in context (2015) (12)
- Mapping the multiscale structure of biological systems. (2021) (12)
- An Integrated Map of HIV-Human Protein Complexes that Facilitate Viral Infection (2014) (12)
- The Protein Architecture of Human Secretory Vesicles Reveals Differential Regulation of Signaling Molecule Secretion by Protein Kinases (2012) (12)
- Interpretation of cancer mutations using a multiscale map of protein systems (2021) (12)
- A convergent molecular network underlying autism and congenital heart disease. (2021) (11)
- Modeling Transcriptome Dynamics in a Complex World (2012) (11)
- The Dfm1 Derlin Is Required for ERAD Retrotranslocation of Integral Membrane Proteins. (2018) (11)
- Reductions in Gray Matter Linked to Epigenetic HIV-Associated Accelerated Aging. (2021) (11)
- The Cytoscape Automation app article collection (2018) (11)
- Integrative Network-based Association Studies: Leveraging cell regulatory models in the post-GWAS era (2011) (11)
- Interactome networks: the state of the science (2006) (10)
- Quantitative Proteomics Reveal ATM Kinase-dependent Exchange in DNA Damage Response Complexes (2012) (10)
- Chemogenetic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition (2015) (10)
- ndexr—an R package to interface with the network data exchange (2018) (9)
- Epigenetic Markers of Aging Predict the Neural Oscillations Serving Selective Attention. (2019) (9)
- De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences (2020) (9)
- On entropy and information in gene interaction networks (2018) (9)
- Deep distributed computing to reconstruct extremely large lineage trees (2022) (9)
- The Cytoscape app article collection (2014) (8)
- Synthetic essentiality of metabolic regulator PDHK1 in PTEN-deficient cells and cancers (2018) (8)
- Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues. (2015) (7)
- Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning (2019) (7)
- Association of Epigenetic Metrics of Biological Age With Cortical Thickness (2020) (7)
- Quantitative translation of dog-to-human aging by conserved remodeling of epigenetic networks (2019) (7)
- Ideker Perturbed Metabolic Network Integrated Genomic and Proteomic Analyses of a Systematically (2013) (7)
- Deep functional synthesis: a machine learning approach to gene functional enrichment (2019) (7)
- 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 (2007) (7)
- Systematic Gene-to-Phenotype Arrays: A High-Throughput Technique for Molecular Phenotyping. (2018) (6)
- Transcriptional responses to DNA damage. (2019) (6)
- Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas (2018) (6)
- Epigenetic aging: Biological age prediction and informing a mechanistic theory of aging (2022) (6)
- Mapping cell structure across scales by fusing protein images and interactions (2020) (6)
- Stress-induced aberrations in sensory processing predict worse cognitive outcomes in healthy aging adults (2021) (6)
- Classifying tumors by supervised network propagation (2018) (5)
- Combinatorial CRISPR-Ca s 9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP 1-NRF 2 Regulatory Axis (2018) (5)
- Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers (2019) (5)
- Correcting CRISPR for copy number (2017) (5)
- Comparison of Protein-Protein Interaction Confidence Assignment Schemes (2005) (5)
- A Blueprint for Systems Biology. (2019) (4)
- Adaptive laboratory evolution in S. cerevisiae highlights role of transcription factors in fungal xenobiotic resistance (2022) (4)
- Deciphering signaling specificity with interpretable deep neural networks (2018) (4)
- Development of a systems approach for the analysis of toxicogenomic data (2007) (4)
- A genetic interaction map centered on cohesin reveals auxiliary factors involved in sister chromatid cohesion in S. cerevisiae (2020) (4)
- The Hallmarks of Cancer Revisited Through Systems Biology and Network Modelling (2011) (3)
- PKC ε regulates ATF 2 availability to alter mitochondrial permeability following genotoxic stress (2013) (3)
- Abstract 3821: A prognostic model of head and neck cancer ties TP53 mutation to 3p loss (2014) (3)
- HTRA1 REGULATES ANGIOGENESIS THROUGH TGF- FAMILY MEMBER GDF6 (2011) (3)
- Combinatorial CRISPR-Cas9 Knockout Screen (2017) (3)
- Defining the Yeast Resistome through in vitro Evolution and Whole Genome Sequencing (2021) (3)
- Targeting the mTOR Signaling Circuitry in Head and Neck Cancer (2017) (3)
- Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment (2017) (3)
- Identifying persistent structures in multiscale ‘omics data (2020) (2)
- A unified GenomeSpace recipe to identify essential genes and associated subnetworks from Genome-Scale CRISPR-Cas9 knockout screens (2018) (2)
- Visualization and Integration of Protein Interaction Networks”, in Protein-Protein Interactions Second Edition: A Molecular Cloning Manual, E. Golemis and P. Adams eds (2005) (2)
- Common genetic variation in the germline influences where and how tumors develop (2017) (2)
- Forging New Ties between E. coli Genes (2008) (2)
- Electrical activity between skin cells regulates melanoma initiation (2021) (2)
- Erratum to: Network-driven plasma proteomics expose molecular changes in the Alzheimer’s brain (2016) (2)
- Unexpected growth of a classic yeast auxotroph (2022) (2)
- De novo emergence of adaptive membrane proteins from thymine-rich intergenic sequences (2019) (2)
- Strategies for Network GWAS Evaluated Using Classroom Crowd Science. (2019) (2)
- Data collection and analysis in systems biology (2004) (1)
- , Systematically Perturbed Metabolic Network Integrated Genomic and Proteomic Analyses of a (2010) (1)
- Roded Sharan Protein networks in disease (2008) (1)
- Biomedical technology and the clinic of the future. (2011) (1)
- Evolution and divergence of herpesviral protein interaction networks (2009) (1)
- Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes (2017) (1)
- A genetic interaction map centered on cohesin reveals auxiliary factors in sister chromatid cohesion. (2020) (1)
- The Cancer Cell Map Initiative (2016) (1)
- Genetic dissection of complex traits using hierarchical biological knowledge (2021) (1)
- Epigenetic aging is associated with aberrant neural oscillatory dynamics serving visuospatial processing in people with HIV (2022) (1)
- Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. (2014) (1)
- On the illusion of auxotrophy: met15Δ yeast cells can grow on inorganic sulfur, thanks to the previously uncharacterized homocysteine synthase Yll058w (2022) (1)
- Unveiling unexpected complexity and multipotentiality of early heart fields (2021) (1)
- Cytoscape tools for the web age : D 3 . js and Cytoscape (2021) (1)
- Uncovering Regulatory Pathways with Expression Quantitative Trait Loci (2007) (1)
- Proceedings of the joint 2006 satellite conference on Systems biology and computational proteomics (2006) (1)
- A global transcriptional network connecting noncoding mutations to changes in tumor gene expression (2018) (1)
- Protein Interaction Networks (2006) (1)
- Abstract 1310: Systematic evaluation of gene networks for discovery of disease genes (2018) (1)
- Abstract 129: RAD17 loss of function is synthetically lethal with the checkpoint kinase inhibitors AZD7762 or MK-1775 (2015) (1)
- Faculty Opinions recommendation of Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function. (2012) (1)
- Rare variant phasing using paired tumor:normal sequence data (2019) (1)
- Association of methylation of genes in the taurine/hypotaurine pathway with worse prognosis in renal cell carcinoma. (2013) (1)
- Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions (2017) (0)
- Abstract 1317: Multi-scale mapping of the physical and functional architecture of the cancer cell (2018) (0)
- Author Correction: De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences (2021) (0)
- Network-driven plasma proteomics expose molecular changes in the Alzheimer’s brain (2016) (0)
- Abstract 178: Desmosome mutations in melanoma promote cellular proliferation and disease progression (2021) (0)
- Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers (2019) (0)
- Parallel genome-wide screens identify synthetic viable interactions between the BLM helicase complex and Fanconi anemia (2017) (0)
- Abstract 369: Network-based stratification of thyroid cancer (2014) (0)
- Abstract 5727: MHC II complements MHC I in shaping the mutational landscape of tumors (2018) (0)
- Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas (2018) (0)
- Systematic Evaluation of M olecular Networks for Discovery of Disease Genes Graphical (2018) (0)
- Abstract 1159: Predicting clinical drug responses using a few-shot learning-based interpretable AI (2022) (0)
- Ultrahigh-Density Screens for Genome-Wide Yeast EMAPs in a Single Plate. (2019) (0)
- Abstract 3299: High-throughput combinatorial CRISPR-Cas9 gene knockout reveals most genetic interactions are context dependent (2018) (0)
- Abstract A14: Network-based stratification: Combining genome-scale somatic mutation profiles with genetic interaction networks to identify clinically relevant subtypes in high grade serous ovarian carcinoma (2013) (0)
- Building Hierarchical Models of the Cell from Genomics Data (2017) (0)
- Mapping the common gene networks that underlie related diseases. (2023) (0)
- Protein Sequencing (2020) (0)
- Promise and reality of systems biology in elucidating cellular behavior: Studying global regulation in yeast (2008) (0)
- NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange (2022) (0)
- A census of pathway maps in cancer systems biology (2020) (0)
- Systematic Gene-to-Phen otype Arrays : A High-Throughput Technique for Molecular Phenotyping Graphical Abstract Highlights (2018) (0)
- Abstract IA24: Are tumors predictable? Inherited immune variation constrains tumor evolution (2018) (0)
- An Ontology of Functions and Processes Derived from Molecular Networks (2014) (0)
- Decoding of persistent multiscale structures in complex biological networks. (2020) (0)
- Rare variant phasing using paired tumor:normal sequence data (2019) (0)
- Deciphering Signaling Specificity with Deep Neural Networks (2018) (0)
- Abstract 2078: A multiscale map of DNA damage response in human cells (2021) (0)
- Lecture 5 Probabilistic Models and Motif Discovery (1998) (0)
- Author Correction: De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences (2021) (0)
- In vitro evolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells (2022) (0)
- Deep distributed computing to reconstruct extremely large lineage trees (2022) (0)
- Tool DDOT : A Swiss Army Knife for Investigating Data-Driven Biological Ontologies Graphical (2019) (0)
- Transcriptional control (SY4-4) Chairpersons: Toshinori Nakayama, Ellen Rothenberg (2010) (0)
- Abstract 636: Prediction of therapeutic response via data-driven maps of tumor cell architecture (2022) (0)
- Gaia Novarino Common Neurodegenerative Disorders Exome Sequencing Links Corticospinal Motor Neuron Disease to (2014) (0)
- A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression (2017) (0)
- The Thinking Man's Cell Dennis Bray Wetware: A Computer in Every Living Cell 2009 Yale University Press New Haven, CT, USA 267 pp. $28.00 (2009) (0)
- Abstract PL02-04: Decoding patient genomes through the hierarchical pathway architecture of the cancer cell (2018) (0)
- New Opportunities and Challenges in Network Biology (2012) (0)
- Abstract IA16: Systematic mapping and modeling of genetic interaction networks in cancer cells (2017) (0)
- Prospecting whole cancer genomes (2020) (0)
- Assen Roguev , Revealed by an Epistasis Map in Fission Yeast Conservation and Rewiring of Functional Modules (2008) (0)
- Abstract CN05-01: The Cancer Cell Map Initiative: Mapping molecular networks for tumor stratification and treatment (2015) (0)
- subtelomere Dynamic reprogramming of transcription factors to and from the Material (2009) (0)
- Faculty Opinions recommendation of Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. (2010) (0)
- Abstract PO017: HBV alters YAP regulation in liver cancer by remodeling PP2A complexes (2022) (0)
- Faculty Opinions recommendation of Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. (2009) (0)
- Abstract PR08: Combinatorial CRISPR-Cas9 reveals many cancer synthetic lethal interactions are private to cell type (2017) (0)
- Title : Evidence for a common evolutionary rate in metazoan 1 transcriptional networks (2015) (0)
- Abstract 4891: Hepatitis B virus remodels host protein interaction networks to generate distinct cellular dependencies (2020) (0)
- A genetic interaction map centered on cohesin reveals auxiliary factors involved in sister chromatid cohesion in <italic>S. cerevisiae</italic> (2020) (0)
- Fluorescence Imaging in Mice Cancer Genome Atlas Analysis and − Matrix-Metalloproteinases in Head and Neck Carcinoma (2014) (0)
- AMultiscaleMap of the StemCell State in Pancreatic Adenocarcinoma Graphical Abstract Highlights (2019) (0)
- Session Introduction (2004) (0)
- Abstract 4306: Identifying genetic dependencies of replication stress using interpretable artificial intelligence (2023) (0)
- 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) (2007) (0)
- Abstract NG02: A network of deeply conserved synthetic-lethal interactions for exploration of precision cancer therapy (2016) (0)
- Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers (2019) (0)
- Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls (2017) (0)
- Offset correction techniques for imaging sensors using random dither information (1995) (0)
- Abstract LB-068: Classification of cancer by synthesis of rare non-coding mutations within recurrent epigenetic and protein networks (2016) (0)
- Abstract 2133: Systematic mapping of genetic interactions in human cancer cells reveals context dependent cancer signaling pathways (2021) (0)
- A platinum-resistant subtype of high-grade serous ovarian cancer identified by a network of somatic mutations. (2017) (0)
- Protein Expression (2020) (0)
- Abstract AP23: A PLATINUM–RESISTANT SUBTYPE OF HIGH–GRADE SEROUS OVARIAN CANCER IDENTIFIED BY A NETWORK OF SOMATIC MUTATIONS (2017) (0)
- Typing tumors using pathways selected by somatic evolution (2018) (0)
- Visualization and Analysis of Biological Networks and Models (2015) (0)
- The Cytoscape Automation app article collection [version 1; referees: Not peer reviewed] (2018) (0)
- 2 A MULTI-CONDITIONAL GeNeTIC INTeRACTION MAP TO DISSeCT DNA DAMAGe ReSPONSe PAThwAyS (2013) (0)
- 6 Sae2 and PPh3 cooPerate to Promote dna rePair and checkPoint recovery (2013) (0)
- The Cancer Cell Mapping Initiative (2022) (0)
- Abstract B34: High-throughput synthetic lethal interaction screening in model organisms as a strategy for the identification of novel therapeutic targets in cancer (2014) (0)
- Development and commercialization of a designed regulatory protein ( DRP ) that activates the Erythropoietin gene in the treatment of anemia PI : (2012) (0)
- Abstract 3039: Combinatorial CRISPR-Cas9 gene knockout to enable genetic interaction mapping in human cells (2017) (0)
- Cross-species synthetic lethal interaction screening as a strategy for the identification of novel therapeutic targets in cancer. (2013) (0)
- Author Index (2002) (0)
- Author Correction: A census of pathway maps in cancer systems biology (2021) (0)
- Hybridization and Post-Hybridization Washing (2002) (0)
- Abstract IA-09: Mapping cell structure across scales by fusing protein images and interactions (2021) (0)
- Microsoft Word-Final Souvenir Science and Scientist-2016.docx (2016) (0)
- Strategies for Network GWAS Evaluated Using Classroom Crowd Science. (2019) (0)
- Adaptive laboratory evolution in S. cerevisiae highlights role of transcription factors in fungal xenobiotic resistance (2022) (0)
- Interactome-Based Molecular Prognosis of Chronic Lymphocytic Leukemia (2008) (0)
- Faculty Opinions recommendation of Genotype to phenotype: a complex problem. (2010) (0)
- Abstract 217: Mutations in iron-sulfur cluster proteins are associated with decreased bladder cancer cell senescence and improved survival outcomes (2021) (0)
- HBV rewires liver cancer signaling by altering PP2A complexes (2023) (0)
- Protein Network Comparative Genomics (2006) (0)
- SYSTEMS BIOLOGY: NETWORKS (2010) (0)
- NeddylatioN affects cell cycle coNtrol aNd geNome iNtegrity (2013) (0)
- Uncovering Tumorigenesis Circuitry with Combinatorial CRISPR (2021) (0)
- Abstract P6-06-01: Analyzing the physical and functional protein interaction landscape of breast cancer (2019) (0)
- ISMB 2008 Organization (2008) (0)
- HiDeF: identifying persistent structures in multiscale ‘omics data (2021) (0)
- Supporting Online Material for Rewiring of Genetic Networks in Response to DNA Damage (2010) (0)
- Discovering biomarkers of chemotherapy resistance using in vitro evolution in haploid human cells (2020) (0)
- Abstract PHB03: A hierarchical model of DNA repair inferred from omics-scale genetic interaction data reveals the dynamics of DNA damage induction (2020) (0)
- Abstract C006: DrugCell: A visible neural network to guide precision medicine (2019) (0)
- Author response: Evidence for a common evolutionary rate in metazoan transcriptional networks (2015) (0)
- UNDERSTANDING THE IMPACT OF PSYCHIATRIC GENOMES ON THE HIERARCHY OF BIOLOGICAL PATHWAYS AND SYSTEMS (2019) (0)
- Abstract 2308: The protein interaction landscape of breast cancer (2021) (0)
- Abstract 1925: DrugCell: A visible neural network to guide personalized medicine (2020) (0)
- Differential analysis of high-throughput quantitative genetic interaction data (2012) (0)
- Genome-Wide Dynamic Evaluation of the UV-Induced DNA Damage Response (2020) (0)
- Abstract 223: Using physical, genetic and integrated cancer cell maps to investigate head and neck cancer and breast cancer (2020) (0)
- DNA methylation aging clocks: challenges and recommendations (2019) (0)
- Author Correction: A census of pathway maps in cancer systems biology (2021) (0)
- Faculty Opinions recommendation of Charting the molecular network of the drug target Bcr-Abl. (2009) (0)
- Erratum Bioengineering and Systems Biology (2006) (0)
- Protein Networks and Analysis of Global Gene Expression (2007) (0)
- Proceedings of the 2005 joint annual satellite conference on Systems biology and regulatory genomics (2005) (0)
- Target deconvolution using in vitro evolution in haploid human cells (2020) (0)
- Explorer Evolutionarily Conserved Herpesviral Protein Interaction Networks (2017) (0)
- Additional data file 5 (2003) (0)
- Abstract PR14: A multiscale map of recurrently mutated systems in cancer (2020) (0)
- Journal Pre-proof met15Δ grow on thanks to the previously homocysteine synthase Yll058w (0)
- A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. (2017) (0)
- COMPUTATIONAL AND SYMBOLIC SYSTEMS BIOLOGY (2003) (0)
- pathways that associate with disease progression Subnetwork-based analysis of chronic lymphocytic leukemia identifies (2012) (0)
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