List of works - Justin Guinney

A 10-gene progenitor cell signature predicts poor prognosis in lung adenocarcinoma.

scientific article

A DREAM Challenge to Build Prediction Models for Short-Term Discontinuation of Docetaxel in Metastatic Castration-Resistant Prostate Cancer

scientific article published on 01 November 2017

A Machine-Learning Tool Concurrently Models Single Omics and Phenome Data for Functional Subtyping and Personalized Cancer Medicine

scientific article published on 30 September 2020

A cancer pharmacogenomic screen powering crowd-sourced advancement of drug combination prediction

A clinically and genomically annotated nerve sheath tumor biospecimen repository

scientific article published on 19 June 2020

A high-throughput molecular data resource for cutaneous neurofibromas.

scientific article

Alternative models for sharing confidential biomedical data

article by Justin Guinney et al published 9 May 2018 in Nature Biotechnology

American Association for Cancer Research Project Genomics Evidence Neoplasia Information Exchange: From Inception to First Data Release and Beyond—Lessons Learned and Member Institutions’ Perspectives

scientific article published in November 2018

Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles

scientific article

BRAF V600E Mutant Colorectal Cancer Subtypes Based on Gene Expression

scientific article published on 27 June 2016

CRI iAtlas: an interactive portal for immuno-oncology research

scientific article published on 24 August 2020

CTCF haploinsufficiency destabilizes DNA methylation and predisposes to cancer

scientific article

Colorectal Cancer Consensus Molecular Subtypes Translated to Preclinical Models Uncover Potentially Targetable Cancer Cell Dependencies

scientific article published on 14 December 2017

Colorectal premalignancy is associated with consensus molecular subtypes 1 and 2

scientific article published on 01 October 2018

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

scientific article published on 06 November 2018

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.

scientific article published on 17 June 2019

Community mining of open clinical trial data.

scientific article published on 13 September 2017

Consensus molecular subtypes and the evolution of precision medicine in colorectal cancer

scientific article published on 4 January 2017

Consensus molecular subtypes and the evolution of precision medicine in colorectal cancer

scientific article published on 01 March 2017

Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge

scientific article

Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge

scientific article published on 14 September 2021

Cutaneous neurofibromas in the genomics era: current understanding and open questions

scientific article published on 26 April 2018

Database of genomic biomarkers for cancer drugs and clinical targetability in solid tumors

scientific article

Engaging a community to enable disease-centric data sharing with the NF Data Portal

scientific article published on 13 December 2019

Estimating variable structure and dependence in multitask learning via gradients

article

Evaluation of Combined Artificial Intelligence and Radiologist Assessment to Interpret Screening Mammograms

scientific article published on 02 March 2020

Evidence for type II cells as cells of origin of K-Ras-induced distal lung adenocarcinoma

scientific article published on 12 March 2012

F-Seq: a feature density estimator for high-throughput sequence tags

scientific article

Functional precision medicine identifies novel druggable targets and therapeutic options in head and neck cancer.

scientific article published on 29 March 2018

GSVA: gene set variation analysis for microarray and RNA-seq data.

scientific article

Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data

scientific article published on 24 September 2020

Genome-wide methylation profiles reveal quantitative views of human aging rates

scientific article

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

scientific article published on August 2017

Genomic determinants of protein abundance variation in colorectal cancer cells

Genomic strategy for targeting therapy in castration-resistant prostate cancer

scientific article

Impact of bioinformatic procedures in the development and translation of high-throughput molecular classifiers in oncology.

scientific article published on 18 June 2013

Impact of centralization on aCGH-based genomic profiles for precision medicine in oncology

scientific article

Improving breast cancer survival analysis through competition-based multidimensional modeling

scientific article

Inferring causal molecular networks: empirical assessment through a community-based effort

scientific article

Integrating genetic association, genetics of gene expression, and single nucleotide polymorphism set analysis to identify susceptibility Loci for type 2 diabetes mellitus

scientific article

Integrative Analysis Identifies Candidate Tumor Microenvironment and Intracellular Signaling Pathways that Define Tumor Heterogeneity in NF1

scientific article published on 21 February 2020

KRAS mutation and Consensus Molecular Subtypes 2 and 3 are independently associated with reduced immune infiltration and reactivity in colorectal cancer.

scientific article published on 23 October 2017

Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

scientific article published on 02 October 2020

Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data

scientific article published on 3 March 2021

Modeling RAS phenotype in colorectal cancer uncovers novel molecular traits of RAS dependency and improves prediction of response to targeted agents in patients

scientific article

Modeling cancer progression via pathway dependencies

scientific article

Molecular markers identify subtypes of stage III colon cancer associated with patient outcomes

scientific article

Multi-targeting Drug Community Challenge

scientific article published in December 2017

Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease

scientific article published on 14 February 2020

PERSONALIZED HYPOTHESIS TESTS FOR DETECTING MEDICATION RESPONSE IN PARKINSON DISEASE PATIENTS USING iPHONE SENSOR DATA.

scientific article

Pharmacological and genomic profiling of neurofibromatosis type 1 plexiform neurofibroma-derived schwann cells.

scientific article published on 12 June 2018

Piloting a model-to-data approach to enable predictive analytics in health care through patient mortality prediction

scientific article published on 08 July 2020

Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data

scientific article

Prediction of overall survival in stage II and III colon cancer beyond TNM system: a retrospective, pooled biomarker study

scientific article

Predictive genes in adjacent normal tissue are preferentially altered by sCNV during tumorigenesis in liver cancer and may rate limiting

scientific article (publication date: 2011)

Probing the chemical-biological relationship space with the Drug Target Explorer

Relative contribution of clinicopathological variables, genomic markers, transcriptomic subtyping and microenvironment features for outcome prediction in stage II/III colorectal cancer

scientific article published on 01 October 2019

Reply to the letter to the editor 'Including lynch syndrome in personalized prognostication and follow-up of stage II and III colon cancer' by Sciallero et al.

scientific article published on 2 August 2017

Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges

scientific article published on 10 September 2019

Social interactomes for enabling research communities

scientific article published on November 2014

Society for Immunotherapy of Cancer clinical and biomarkers data sharing resource document: Volume I-conceptual challenges

scientific article published on 01 October 2020

Society for Immunotherapy of Cancer clinical and biomarkers data sharing resource document: Volume II-practical challenges

scientific article published on 01 December 2020

Spatiotemporal loss of NF1 in Schwann cell lineage leads to different types of cutaneous neurofibroma susceptible to modification by the Hippo pathway

article

Stepwise group sparse regression (SGSR): gene-set-based pharmacogenomic predictive models with stepwise selection of functional priors

scientific article

Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer

scientific article

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

scientific article published on 01 April 2020

The Immune Landscape of Cancer

scientific article published on 4 April 2018

The Immune Landscape of Cancer

scientific article published on 01 August 2019

The NIH BD2K center for big data in translational genomics

scientific article

The consensus molecular subtypes of colorectal cancer

scientific article

The evolution and multi-molecular properties of NF1 cutaneous neurofibromas originating from C-fiber sensory endings and terminal Schwann cells at normal sites of sensory terminations in the skin

scientific article published on 20 May 2019

Traditional and systems biology based drug discovery for the rare tumor syndrome neurofibromatosis type 2.

scientific article

rCGH: a comprehensive array-based genomic profile platform for precision medicine

scientific article published on 26 December 2015

List of works by Justin Guinney

A 10-gene progenitor cell signature predicts poor prognosis in lung adenocarcinoma.

A DREAM Challenge to Build Prediction Models for Short-Term Discontinuation of Docetaxel in Metastatic Castration-Resistant Prostate Cancer

A Machine-Learning Tool Concurrently Models Single Omics and Phenome Data for Functional Subtyping and Personalized Cancer Medicine

A cancer pharmacogenomic screen powering crowd-sourced advancement of drug combination prediction

A clinically and genomically annotated nerve sheath tumor biospecimen repository

A high-throughput molecular data resource for cutaneous neurofibromas.

Alternative models for sharing confidential biomedical data

American Association for Cancer Research Project Genomics Evidence Neoplasia Information Exchange: From Inception to First Data Release and Beyond—Lessons Learned and Member Institutions’ Perspectives

Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles

BRAF V600E Mutant Colorectal Cancer Subtypes Based on Gene Expression

CRI iAtlas: an interactive portal for immuno-oncology research

CTCF haploinsufficiency destabilizes DNA methylation and predisposes to cancer

Colorectal Cancer Consensus Molecular Subtypes Translated to Preclinical Models Uncover Potentially Targetable Cancer Cell Dependencies

Colorectal premalignancy is associated with consensus molecular subtypes 1 and 2

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.

Community mining of open clinical trial data.

Consensus molecular subtypes and the evolution of precision medicine in colorectal cancer

Consensus molecular subtypes and the evolution of precision medicine in colorectal cancer

Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge

Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge

Cutaneous neurofibromas in the genomics era: current understanding and open questions

Database of genomic biomarkers for cancer drugs and clinical targetability in solid tumors

Engaging a community to enable disease-centric data sharing with the NF Data Portal

Estimating variable structure and dependence in multitask learning via gradients

Evaluation of Combined Artificial Intelligence and Radiologist Assessment to Interpret Screening Mammograms

Evidence for type II cells as cells of origin of K-Ras-induced distal lung adenocarcinoma

F-Seq: a feature density estimator for high-throughput sequence tags

Functional precision medicine identifies novel druggable targets and therapeutic options in head and neck cancer.

GSVA: gene set variation analysis for microarray and RNA-seq data.

Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data

Genome-wide methylation profiles reveal quantitative views of human aging rates

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

Genomic determinants of protein abundance variation in colorectal cancer cells

Genomic strategy for targeting therapy in castration-resistant prostate cancer

Impact of bioinformatic procedures in the development and translation of high-throughput molecular classifiers in oncology.

Impact of centralization on aCGH-based genomic profiles for precision medicine in oncology

Improving breast cancer survival analysis through competition-based multidimensional modeling

Inferring causal molecular networks: empirical assessment through a community-based effort

Integrating genetic association, genetics of gene expression, and single nucleotide polymorphism set analysis to identify susceptibility Loci for type 2 diabetes mellitus

Integrative Analysis Identifies Candidate Tumor Microenvironment and Intracellular Signaling Pathways that Define Tumor Heterogeneity in NF1

KRAS mutation and Consensus Molecular Subtypes 2 and 3 are independently associated with reduced immune infiltration and reactivity in colorectal cancer.

Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data

Modeling RAS phenotype in colorectal cancer uncovers novel molecular traits of RAS dependency and improves prediction of response to targeted agents in patients

Modeling cancer progression via pathway dependencies

Molecular markers identify subtypes of stage III colon cancer associated with patient outcomes

Multi-targeting Drug Community Challenge

Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease

PERSONALIZED HYPOTHESIS TESTS FOR DETECTING MEDICATION RESPONSE IN PARKINSON DISEASE PATIENTS USING iPHONE SENSOR DATA.

Pharmacological and genomic profiling of neurofibromatosis type 1 plexiform neurofibroma-derived schwann cells.

Piloting a model-to-data approach to enable predictive analytics in health care through patient mortality prediction

Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data

Prediction of overall survival in stage II and III colon cancer beyond TNM system: a retrospective, pooled biomarker study

Predictive genes in adjacent normal tissue are preferentially altered by sCNV during tumorigenesis in liver cancer and may rate limiting

Probing the chemical-biological relationship space with the Drug Target Explorer

Probing the chemical-biological relationship space with the Drug Target Explorer

Relative contribution of clinicopathological variables, genomic markers, transcriptomic subtyping and microenvironment features for outcome prediction in stage II/III colorectal cancer

Reply to the letter to the editor 'Including lynch syndrome in personalized prognostication and follow-up of stage II and III colon cancer' by Sciallero et al.

Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges

Social interactomes for enabling research communities

Society for Immunotherapy of Cancer clinical and biomarkers data sharing resource document: Volume I-conceptual challenges

Society for Immunotherapy of Cancer clinical and biomarkers data sharing resource document: Volume II-practical challenges

Spatiotemporal loss of NF1 in Schwann cell lineage leads to different types of cutaneous neurofibroma susceptible to modification by the Hippo pathway

Stepwise group sparse regression (SGSR): gene-set-based pharmacogenomic predictive models with stepwise selection of functional priors

Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

The Immune Landscape of Cancer

The Immune Landscape of Cancer

The NIH BD2K center for big data in translational genomics

The consensus molecular subtypes of colorectal cancer

The evolution and multi-molecular properties of NF1 cutaneous neurofibromas originating from C-fiber sensory endings and terminal Schwann cells at normal sites of sensory terminations in the skin

Traditional and systems biology based drug discovery for the rare tumor syndrome neurofibromatosis type 2.

rCGH: a comprehensive array-based genomic profile platform for precision medicine