List of works by Gary D. Bader

A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling

scientific article published on 7 November 2017

A Progesterone-CXCR4 Axis Controls Mammary Progenitor Cell Fate in the Adult Gland

scientific article published on 19 February 2015

A Progesterone-CXCR4 Axis Controls Mammary Progenitor Cell Fate in the Adult Gland.

scientific article published on 10 March 2015

A brief history of COMBINE

A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules

scientific article

A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals

scientific article published on August 2012

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

scientific article

A draft map of the human proteome

scientific article (publication date: 29 May 2014)

A flexible search system for high-accuracy identification of biological entities and molecules

scientific article published on 12 November 2021

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

scientific article published on 16 January 2020

A predictive model for drug bioaccumulation and bioactivity in Caenorhabditis elegans

scientific article published on 30 May 2010

A reference map of the human binary protein interactome

scientific article published on 08 April 2020

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

scientific article

A specificity map for the PDZ domain family

scientific article

A travel guide to Cytoscape plugins

scientific article

ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells

scientific article published in September 2017

ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells.

scientific article published on 11 July 2017

Abstracts

article by L. Bie et al published 1 April 2013 in Neuro-Oncology

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

scientific article

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

scientific article

Analyzing yeast protein-protein interaction data obtained from different sources

scientific article

Antitumor activity of the novel multi-kinase inhibitor EC-70124 in triple negative breast cancer

scientific article

Approaches to Analyze Protein Interactions.

scientific article

Association analysis identifies 65 new breast cancer risk loci.

scientific article published on 23 October 2017

Attenuation of miR-126 activity expands HSC in vivo without exhaustion.

scientific article

Author-sourced capture of pathway knowledge in computable form using Biofactoid

scientific article published on 03 December 2021

AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations

scientific article published on 15 July 2016

Automated Computational Inference of Multi-protein Assemblies from Biochemical Co-purification Data.

scientific article published in January 2018

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

scientific article published in May 2000

BIND: the Biomolecular Interaction Network Database

scientific article (publication date: 2003)

Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins

scientific article

Biological and therapeutic implications of a unique subtype of NPM1 mutated AML

scientific article published on 16 February 2021

Biological network exploration with Cytoscape 3

scientific article

Bringing order to protein disorder through comparative genomics and genetic interactions

scientific article

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions

scientific article

CD200 expression marks leukemia stem cells in human AML

scientific article published on 01 November 2020

Cardioprotective Signature of Short-Term Caloric Restriction

scientific article

Chromatin is an ancient innovation conserved between Archaea and Eukarya

scientific article

Combined deletion of Pten and p53 in mammary epithelium accelerates triple-negative breast cancer with dependency on eEF2K

scientific article

Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases

scientific article published on 28 July 2009

Compound prioritization methods increase rates of chemical probe discovery in model organisms

scientific article

Comprehensive Analysis of the Human SH3 Domain Family Reveals a Wide Variety of Non-canonical Specificities.

scientific article published on 28 August 2017

Comprehensive identification of mutational cancer driver genes across 12 tumor types

scientific article

Computational Prediction of Protein–Protein Interactions

scientific article published on 14 August 2007

Computational approaches to identify functional genetic variants in cancer genomes

scientific article published on August 2013

Computational prediction of cancer-gene function

scientific article published on 14 December 2006

Coordinate microRNA-mediated regulation of protein complexes in prostate cancer

scientific article

Corrigendum: The BioPAX community standard for pathway data sharing

correction; published 7 December 2010

Cytoscape Web: an interactive web-based network browser

scientific article

Cytoscape app store

scientific article published on 16 April 2013

Cytoscape.js 2023 update: a graph theory library for visualization and analysis

scientific article published in 2023

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

scientific article published on 28 September 2015

DRYGIN: a database of quantitative genetic interaction networks in yeast

scientific article published on 30 October 2009

Delineation of two clinically and molecularly distinct subgroups of posterior fossa ependymoma

scientific article

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

scientific article

Developmental Emergence of Adult Neural Stem Cells as Revealed by Single-Cell Transcriptional Profiling

scientific article published in December 2017

Displaying chemical information on a biological network using Cytoscape

scientific article published on January 2011

Divergent clonal selection dominates medulloblastoma at recurrence

scientific article published on 13 January 2016

Domain-mediated protein interaction prediction: From genome to network

scientific article published on 3 May 2012

Drugst.One — a plug-and-play solution for online systems medicine and network-based drug repurposing

scientific article published in 2024

Dynamic interaction networks in a hierarchically organized tissue

scientific article published on October 2010

Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis.

scientific article published on 15 March 2016

EAG2 potassium channel with evolutionarily conserved function as a brain tumor target

scientific article

EPIC: software toolkit for elution profile-based inference of protein complexes

scientific article published on 15 July 2019

Ectopic miR-125a Expression Induces Long-Term Repopulating Stem Cell Capacity in Mouse and Human Hematopoietic Progenitors

scientific article

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

scientific article

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

scientific article published on July 2014

Enrichment map: a network-based method for gene-set enrichment visualization and interpretation

scientific article

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy

scientific article

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

scientific article published on 11 August 2015

Erratum: Corrigendum: The BioPAX community standard for pathway data sharing

scholarly article published in Nature Biotechnology

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

scientific article published on 15 March 2019

Evolutionary constraint and disease associations of post-translational modification sites in human genomes

scientific article

Exploring biological networks with Cytoscape software

scientific article published in September 2008

Faculty of 1000 evaluation for A comprehensive molecular interaction map of the budding yeast cell cycle

Faculty of 1000 evaluation for A global protein kinase and phosphatase interaction network in yeast

Faculty of 1000 evaluation for Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells

Faculty of 1000 evaluation for Measuring the evolutionary rewiring of biological networks

Faculty of 1000 evaluation for Modeling synthetic lethality

Faculty of 1000 evaluation for Mutual exclusivity analysis identifies oncogenic network modules

Faculty of 1000 evaluation for NOA: a novel Network Ontology Analysis method

Faculty of 1000 evaluation for Predicting selective drug targets in cancer through metabolic networks

Faculty of 1000 evaluation for Quantitative epistasis analysis and pathway inference from genetic interaction data

Faculty of 1000 evaluation for Reverse engineering a signaling network using alternative inputs

Faculty of 1000 evaluation for Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

Faculty of 1000 evaluation for Structure-based prediction of protein-protein interactions on a genome-wide scale

Faculty of 1000 evaluation for Testing the ortholog conjecture with comparative functional genomic data from mammals

Faculty of 1000 evaluation for Toward an understanding of the protein interaction network of the human liver

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

scientific article published on 12 May 2016

From bytes to bedside: data integration and computational biology for translational cancer research

scientific article

Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance

scientific article

Functional complexes between YAP2 and ZO-2 are PDZ domain-dependent, and regulate YAP2 nuclear localization and signalling

scientific article published on December 2010

Functional genomic landscape of cancer-intrinsic evasion of killing by T cells

scientific article published on 23 September 2020

Functional genomics and proteomics: charting a multidimensional map of the yeast cell

scientific article

Functional genomics of intracellular peptide recognition domains with combinatorial biology methods

scientific article

Functional impact of global rare copy number variation in autism spectrum disorders

scientific article published on 15 July 2010

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

scientific article published on 3 January 2013

GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop

scientific article

GeneMANIA prediction server 2013 update

scientific article published on July 2013

GeneMANIA: Fast gene network construction and function prediction for Cytoscape

scientific article published on July 2014

Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition

scientific article

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

scientific article published on 19 July 2007

Global mapping of the yeast genetic interaction network

scientific article

GreedyPlus: An Algorithm for the Alignment of Interface Interaction Networks

scientific article published on 13 July 2015

HOX gene complement and expression in the planarian Schmidtea mediterranea

scientific article published on 30 March 2016

Highlights of B/D-HPP and HPP Resource Pillar Workshops at 12th Annual HUPO World Congress of Proteomics: September 14-18, 2013, Yokohama, Japan

scientific article published in May 2014

How to visually interpret biological data using networks

scientific article

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

scientific article published on 8 April 2014

Hypophosphorylated pRb knock-in mice exhibit hallmarks of aging and vitamin C-preventable diabetes

scientific article published on 13 January 2022

IL-7 coordinates proliferation, differentiation and Tcra recombination during thymocyte β-selection.

scientific article

Identification of CD146 as a marker enriched for tumor-propagating capacity reveals targetable pathways in primary human sarcoma

scientific article published on 26 October 2015

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

scientific article

Inhibition of Dopamine Receptor D4 Impedes Autophagic Flux, Proliferation, and Survival of Glioblastoma Stem Cells

scientific article

Inhibition of the Mitochondrial Protease ClpP as a Therapeutic Strategy for Human Acute Myeloid Leukemia.

scientific article published on June 2015

Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors

scientific article

Integrated analysis of proteome, phosphotyrosine-proteome, tyrosine-kinome, and tyrosine-phosphatome in acute myeloid leukemia

scientific article published on 7 February 2017

Integrated genomics elucidates relative spatial homogeneity of embryonal brain tumors.

scientific article

Integration of biological networks and gene expression data using Cytoscape

scientific article (publication date: 2007)

Integrative Cancer Pharmacogenomics to Infer Large-Scale Drug Taxonomy

scientific article

Integrative pathway dissection of molecular mechanisms of moxLDL-induced vascular smooth muscle phenotype transformation

scientific article

Intercellular network structure and regulatory motifs in the human hematopoietic system

scientific article

International network of cancer genome projects

scientific article

Intertumoral Heterogeneity within Medulloblastoma Subgroups

scientific article published on June 2017

Leveraging increased cytoplasmic nucleoside kinase activity to target mtDNA and oxidative phosphorylation in AML.

scientific article published on 10 March 2017

List of Contributors

Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes

scientific article

MB-21INTEGRATED GENOMICS ELUCIDATES RELATIVE SPATIAL HOMOGENEITY OF EMBRYONAL BRAIN TUMORS.

scientific article published on 21 April 2015

MIMP: predicting the impact of mutations on kinase-substrate phosphorylation.

scientific article published on 4 May 2015

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

scientific article

Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities

scientific article published on 19 June 2018

Mapping the Hsp90 genetic interaction network in Candida albicans reveals environmental contingency and rewired circuitry

scientific article

Mapping the cellular response to small molecules using chemogenomic fitness signatures

scientific article

Medical and socio-professional impact of insomnia.

scientific article published in September 2002

Medulloblastoma Arises from the Persistence of a Rare and Transient Sox2+ Granule Neuron Precursor

scientific article published on 01 April 2020

Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE).

scientific article published on November 2011

Metabolic adaptation to chronic inhibition of mitochondrial protein synthesis in acute myeloid leukemia cells

scientific article

Metabolomic profiling in liver of adiponectin-knockout mice uncovers lysophospholipid metabolism as an important target of adiponectin action.

scientific article published on 27 April 2015

Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups

scientific article

Molecular subgroups of atypical teratoid rhabdoid tumours in children: an integrated genomic and clinicopathological analysis

scientific article

Multiple genetic interaction experiments provide complementary information useful for gene function prediction

scientific article

Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells

scientific article published on April 2016

NetMatchStar: an enhanced Cytoscape network querying app

scientific article published on 5 August 2015

NetPath: a public resource of curated signal transduction pathways

scientific article

NetSlim: high-confidence curated signaling maps

scientific article (publication date: 2011)

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

scientific article

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

scientific article

PRMT5 inhibition disrupts splicing and stemness in glioblastoma

scientific article published on 12 February 2021

PSICQUIC and PSISCORE: accessing and scoring molecular interactions

scientific article (publication date: 29 June 2011)

Pathway Commons, a web resource for biological pathway data

scientific article

Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps

scientific article

Pathway and network analysis of cancer genomes

scientific article (publication date: July 2015)

Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap

scientific article published on 01 February 2019

Pathway information for systems biology

scientific article

Phosphorylation sites of higher stoichiometry are more conserved

Playing tag with the yeast proteome ⬇️

scientific article published on November 1, 2003

Positive selection of tyrosine loss in metazoan evolution.

scientific article published on 9 July 2009

Potential Therapeutic Targets for Lung Repair During Human Ex Vivo Lung Perfusion

scientific article published on 17 March 2020

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

article

PreBIND and Textomy--mining the biomedical literature for protein-protein interactions using a support vector machine

scientific article

Predicting PDZ domain mediated protein interactions from structure

scientific article

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

scientific article published on 9 February 2016

Prediction and experimental characterization of nsSNPs altering human PDZ-binding motifs

scientific article

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

scientific article (publication date: 2015)

Protein complexes are central in the yeast genetic landscape

scientific article

Proteome scanning to predict PDZ domain interactions using support vector machines ⬇️

scientific article published on October 12, 2010

Quantitative analysis of fitness and genetic interactions in yeast on a genome scale

scientific article

Quiescent sox2(+) cells drive hierarchical growth and relapse in sonic hedgehog subgroup medulloblastoma

scientific article published on 19 June 2014

RB1 deficiency in triple-negative breast cancer induces mitochondrial protein translation

scientific article published on 29 August 2016

Rapid evolution of functional complexity in a domain family

scientific article

Relapse-Fated Latent Diagnosis Subclones in Acute B Lineage Leukemia Are Drug Tolerant and Possess Distinct Metabolic Programs

scientific article published on 21 February 2020

SC-05DOPAMINE RECEPTOR ANTAGONISTS ARE SELECTIVE INHIBITORS OF GLIOBLASTOMA STEM CELLS THROUGH IMPAIRMENT OF AUTOPHAGY

SH3 interactome conserves general function over specific form.

scientific article published in January 2013

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

scientific article

Seventeen-gene signature from enriched Her2/Neu mammary tumor-initiating cells predicts clinical outcome for human HER2+:ERα- breast cancer

scientific article published on 28 March 2012

Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations

scientific article published in Nature Communications

Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity

scientific article

Single-cell transcriptomic profiling of the aging mouse brain

scientific article published on 24 September 2019

Social Network: a Cytoscape app for visualizing co-authorship networks

scientific article published on 5 August 2015

Spatial heterogeneity in medulloblastoma

scientific article published on 10 April 2017

Specifications of Standards in Systems and Synthetic Biology

scientific article published on 04 September 2015

Specifications of Standards in Systems and Synthetic Biology

scientific article published in June 2015

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

scientific article published on 18 December 2016

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

scientific article published in September 2016

Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024

Sphingosine-1-phosphate receptor 3 potentiates inflammatory programs in normal and leukemia stem cells to promote differentiation

scientific article published on 01 December 2020

Subgroup-specific structural variation across 1,000 medulloblastoma genomes

scientific article

Systematic analysis of somatic mutations impacting gene expression in 12 tumour types

scientific article

Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers

scientific article

Systematic genetic analysis with ordered arrays of yeast deletion mutants

scientific article

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

scientific article (publication date: 10 January 2002)

Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy

scientific article published on 31 October 2014

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

scientific article published on 09 September 2020

Temporal profiling of therapy resistance in human medulloblastoma identifies novel targetable drivers of recurrence

scientific article published on 08 December 2021

Ten Simple Rules for Developing Public Biological Databases

scientific article

The BioPAX Validator

scientific article

The BioPAX community standard for pathway data sharing

scientific article (publication date: September 2010)

The Biomolecular Interaction Network Database in PSI-MI 2.5.

scientific article

The Cytoscape Automation app article collection.

scientific article

The Cytoscape app article collection.

scientific article published on July 2014

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

scientific article (publication date: July 2010)

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data

scientific article (publication date: February 2004)

The Human Cell Atlas White Paper ⬇️

journal article from 'arXiv:1810.05192 [q-bio]' published in 2018

The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community

scientific article published on 21 December 2012

The genetic landscape of a cell

scientific article

The health care and life sciences community profile for dataset descriptions

scientific article (publication date: 2016)

The health care and life sciences community profile for dataset descriptions

The health care and life sciences community profile for dataset descriptions

The health care and life sciences community profile for dataset descriptions

article published in 2016

The minimum information required for reporting a molecular interaction experiment (MIMIx).

scientific article published on August 2007

The mitochondrial peptidase, neurolysin, regulates respiratory chain supercomplex formation and is necessary for AML viability

scientific article published on 01 April 2020

The mutational landscape of phosphorylation signaling in cancer

scientific article published on 02 October 2013

The reactome pathway knowledgebase 2022

scientific article published on 14 October 2021

The transcriptional landscape of Shh medulloblastoma

scientific article published on 19 March 2021

Too many roads not taken

scientific article

Towards reliable named entity recognition in the biomedical domain

scientific article published on 01 January 2020

Tracing the origins of relapse in acute myeloid leukaemia to stem cells.

scientific article published on 28 June 2017

Transcriptomic analysis reveals abnormal muscle repair and remodeling in survivors of critical illness with sustained weakness

scientific article published on 14 July 2016

Transfer learning for biomedical named entity recognition with neural networks

scientific article from bioRxiv

Transfer learning for biomedical named entity recognition with neural networks.

scientific article published in Bioinformatics

Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods

scientific article

Uncovering the Contribution of Moderate-Penetrance Susceptibility Genes to Breast Cancer by Whole-Exome Sequencing and Targeted Enrichment Sequencing of Candidate Genes in Women of European Ancestry

scientific article published on 11 July 2022

Using biological pathway data with paxtools

scientific article

Visualizing gene-set enrichment results using the Cytoscape plug-in enrichment map

scientific article published on 01 January 2011

Wnt activation as a therapeutic strategy in medulloblastoma

scientific article published on 28 August 2020

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

scientific article

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

scientific article

clusterMaker: a multi-algorithm clustering plugin for Cytoscape

scientific article

miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells

scientific article published on 20 January 2016

miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells.

scientific article published on April 2016

netDx: Interpretable patient classification using integrated patient similarity networks

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

scientific article published on 22 January 2021

netDx: interpretable patient classification using integrated patient similarity networks

scientific article published on 14 March 2019

scClustViz - Single-cell RNAseq cluster assessment and visualization

scientific article published on 21 September 2018

scNetViz: from single cells to networks using Cytoscape

scientific article published on 07 June 2021

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