List of works - Yuan Ji

A BAYESIAN NONPARAMETRIC MODEL FOR RECONSTRUCTING TUMOR SUBCLONES BASED ON MUTATION PAIRS.

scientific article published on January 2016

A Bayesian Graphical Model for Integrative Analysis of TCGA Data

scientific article

A Bayesian Model for SNP Discovery Based on Next-Generation Sequencing Data.

scientific article

A Bayesian hierarchical model for inference across related reverse phase protein arrays experiments

scientific article published on January 2014

A Bayesian interval dose-finding design addressingOckham's razor: mTPI-2

scientific article published on 27 April 2017

A Bayesian random partition model for sequential refinement and coagulation

scientific article published on 09 April 2019

A Nonparametric Bayesian Model for Local Clustering with Application to Proteomics

scientific article published on January 2013

A Nonparametric Bayesian Model for Nested Clustering

scientific article published on January 2016

A Time‐Series DDP for Functional Proteomics Profiles ⬇️

scientific article published on January 5, 2012

A decision-theoretic phase I-II design for ordinal outcomes in two cycles

scientific article published on 9 November 2015

A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samples

scientific article

A subgroup cluster-based Bayesian adaptive design for precision medicine

scientific article published on 24 October 2016

AAA: triple adaptive Bayesian designs for the identification of optimal dose combinations in dual-agent dose finding trials.

scientific article

Accuracy of RNA-Seq and its dependence on sequencing depth

scientific article

An integrated dose-finding tool for phase I trials in oncology

scientific article published on 28 September 2015

An oncolytic adenovirus targeting TGFβ inhibits pro-tumorigenic signals and produces immune activation: A novel approach to enhance anti-PD-1 and anti-CTLA-4 therapy

scientific article published on 01 July 2019

BM-BC: a Bayesian method of base calling for Solexa sequence data

scientific article

BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data

scientific article

BM-SNP: A Bayesian Model for SNP Calling Using High Throughput Sequencing Data.

scientific article

BM-map: Bayesian mapping of multireads for next-generation sequencing data

scientific article

Bayclone: Bayesian nonparametric inference of tumor subclones using NGS data

scientific article

Bayesian Approaches to Subgroup Analysis and Related Adaptive Clinical Trial Designs

scientific article published on 24 October 2019

Bayesian Dose-Finding in Two Treatment Cycles Based on the Joint Utility of Efficacy and Toxicity

scientific article published on June 2015

Bayesian Hierarchical Model for Differential Gene Expression Using RNA-seq Data

scientific article published on May 2015

Bayesian estimation of inverse dose response

scientific article published on 19 March 2008

Bayesian graphical models for computational network biology.

scientific article published on 21 March 2018

Bayesian hierarchical models for protein networks in single-cell mass cytometry

scientific article

Bayesian inference for intratumour heterogeneity in mutations and copy number variation

scientific article published on 12 January 2016

Bayesian models based on test statistics for multiple hypothesis testing problems

scientific article published in February 2008

Characterizing Cancer-Specific Networks by Integrating TCGA Data

scientific article

Clustering distributions with the marginalized nested Dirichlet process.

scientific article

Detecting differential patterns of interaction in molecular pathways

scientific article published on 16 December 2014

Discussion of "A hybrid phase I-II/III clinical trial design allowing dose re-optimization in phase III" by Andrew G. Chapple and Peter F. Thall

scientific article published on 03 April 2019

Elevation of Stromal-Derived Mediators of Inflammation Promote Prostate Cancer Progression in African-American Men

scientific article published on 04 September 2018

Heterogeneous reciprocal graphical models.

scientific article published on 10 October 2017

Imaging-Genomic Study of Head and Neck Squamous Cell Carcinoma: Associations Between Radiomic Phenotypes and Genomic Mechanisms via Integration of The Cancer Genome Atlas and The Cancer Imaging Archive

scientific article published on 01 February 2019

MAD Bayes for Tumor Heterogeneity - Feature Allocation with Exponential Family Sampling ⬇️

scientific article

Modeling Protein Expression and Protein Signaling Pathways

scientific article published on January 2011

Nonparametric Bayesian Bi-Clustering for Next Generation Sequencing Count Data

scientific article published on December 2013

On differential gene expression using RNA-Seq data

scientific article

Personalized antibodies for gastroesophageal adenocarcinoma (PANGEA): a phase 2 study evaluating an individualized treatment strategy for metastatic disease

scientific article published on 24 November 2020

Probability intervals of toxicity and efficacy design for dose-finding clinical trials in oncology

scientific article published on 16 December 2020

Propriety conditions for the Bayesian autologistic model - Inference for histone modifications

scientific article published on January 2013

R-TPI: rolling toxicity probability interval design to shorten the duration and maintain safety of phase I trials.

scientific article published on 11 February 2019

Radiogenomics of breast cancer using dynamic contrast enhanced MRI and gene expression profiling

scientific article published on 15 July 2019

RoBoT: a robust Bayesian hypothesis testing method for basket trials

scientific article published on 15 February 2020

Scalable Bayesian Nonparametric Clustering and Classification

scientific article published on 19 July 2019

Semiparametric Bayesian inference for the transmission dynamics of COVID-19 with a state-space model

scientific article published on 15 September 2020

Sparse Bayesian Graphical Models for RPPA Time Course Data

scientific article

Subgroup-Based Adaptive (SUBA) Designs for Multi-Arm Biomarker Trials ⬇️

scientific article published on 17 July 2014

TCGA-Assembler 2: Software Pipeline for Retrieval and Processing of TCGA/CPTAC Data.

scientific article published on 20 December 2017

TEAMS: Toxicity- and Efficacy-based Dose Insertion Design with Adaptive Model Selection for Phase I/II Dose-Escalation Trials in Oncology

scientific article published on 30 June 2015

The evolutionary history of 2,658 cancers

scientific article published on 06 February 2020

The i3+3 design for phase I clinical trials

scientific article published on 15 July 2019

Toward breaking the histone code: bayesian graphical models for histone modifications

scientific article published on 7 June 2013

Toxicity and Efficacy Probability Interval Design for Phase I Adoptive Cell Therapy Dose-Finding Clinical Trials

scientific article published on 14 October 2016

Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data

scientific article

dsPIG: a tool to predict imprinted genes from the deep sequencing of whole transcriptomes ⬇️

scientific article published on October 19, 2012

List of works by Yuan Ji

A BAYESIAN NONPARAMETRIC MODEL FOR RECONSTRUCTING TUMOR SUBCLONES BASED ON MUTATION PAIRS.

A Bayesian Graphical Model for Integrative Analysis of TCGA Data

A Bayesian Model for SNP Discovery Based on Next-Generation Sequencing Data.

A Bayesian hierarchical model for inference across related reverse phase protein arrays experiments

A Bayesian interval dose-finding design addressingOckham's razor: mTPI-2

A Bayesian random partition model for sequential refinement and coagulation

A Nonparametric Bayesian Model for Local Clustering with Application to Proteomics

A Nonparametric Bayesian Model for Nested Clustering

A Time‐Series DDP for Functional Proteomics Profiles ⬇️

A decision-theoretic phase I-II design for ordinal outcomes in two cycles

A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samples

A subgroup cluster-based Bayesian adaptive design for precision medicine

AAA: triple adaptive Bayesian designs for the identification of optimal dose combinations in dual-agent dose finding trials.

Accuracy of RNA-Seq and its dependence on sequencing depth

An integrated dose-finding tool for phase I trials in oncology

An oncolytic adenovirus targeting TGFβ inhibits pro-tumorigenic signals and produces immune activation: A novel approach to enhance anti-PD-1 and anti-CTLA-4 therapy

BM-BC: a Bayesian method of base calling for Solexa sequence data

BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data

BM-SNP: A Bayesian Model for SNP Calling Using High Throughput Sequencing Data.

BM-map: Bayesian mapping of multireads for next-generation sequencing data

Bayclone: Bayesian nonparametric inference of tumor subclones using NGS data

Bayesian Approaches to Subgroup Analysis and Related Adaptive Clinical Trial Designs

Bayesian Dose-Finding in Two Treatment Cycles Based on the Joint Utility of Efficacy and Toxicity

Bayesian Hierarchical Model for Differential Gene Expression Using RNA-seq Data

Bayesian estimation of inverse dose response

Bayesian graphical models for computational network biology.

Bayesian hierarchical models for protein networks in single-cell mass cytometry

Bayesian inference for intratumour heterogeneity in mutations and copy number variation

Bayesian models based on test statistics for multiple hypothesis testing problems

Characterizing Cancer-Specific Networks by Integrating TCGA Data

Clustering distributions with the marginalized nested Dirichlet process.

Detecting differential patterns of interaction in molecular pathways

Discussion of "A hybrid phase I-II/III clinical trial design allowing dose re-optimization in phase III" by Andrew G. Chapple and Peter F. Thall

Elevation of Stromal-Derived Mediators of Inflammation Promote Prostate Cancer Progression in African-American Men

Heterogeneous reciprocal graphical models.

Imaging-Genomic Study of Head and Neck Squamous Cell Carcinoma: Associations Between Radiomic Phenotypes and Genomic Mechanisms via Integration of The Cancer Genome Atlas and The Cancer Imaging Archive

MAD Bayes for Tumor Heterogeneity - Feature Allocation with Exponential Family Sampling ⬇️

Modeling Protein Expression and Protein Signaling Pathways

Nonparametric Bayesian Bi-Clustering for Next Generation Sequencing Count Data

On differential gene expression using RNA-Seq data

Personalized antibodies for gastroesophageal adenocarcinoma (PANGEA): a phase 2 study evaluating an individualized treatment strategy for metastatic disease

Probability intervals of toxicity and efficacy design for dose-finding clinical trials in oncology

Propriety conditions for the Bayesian autologistic model - Inference for histone modifications

R-TPI: rolling toxicity probability interval design to shorten the duration and maintain safety of phase I trials.

Radiogenomics of breast cancer using dynamic contrast enhanced MRI and gene expression profiling

RoBoT: a robust Bayesian hypothesis testing method for basket trials

Scalable Bayesian Nonparametric Clustering and Classification

Semiparametric Bayesian inference for the transmission dynamics of COVID-19 with a state-space model

Sparse Bayesian Graphical Models for RPPA Time Course Data

Subgroup-Based Adaptive (SUBA) Designs for Multi-Arm Biomarker Trials ⬇️

TCGA-Assembler 2: Software Pipeline for Retrieval and Processing of TCGA/CPTAC Data.

TEAMS: Toxicity- and Efficacy-based Dose Insertion Design with Adaptive Model Selection for Phase I/II Dose-Escalation Trials in Oncology

The evolutionary history of 2,658 cancers

The i3+3 design for phase I clinical trials

Toward breaking the histone code: bayesian graphical models for histone modifications

Toxicity and Efficacy Probability Interval Design for Phase I Adoptive Cell Therapy Dose-Finding Clinical Trials

Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data

dsPIG: a tool to predict imprinted genes from the deep sequencing of whole transcriptomes ⬇️