List of works - Pengyi Yang

A benchmark study of simulation methods for single-cell RNA sequencing data

scientific article published on 25 November 2021

A hierarchical approach to removal of unwanted variation for large-scale metabolomics data

scientific article published on 17 August 2021

A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data

scientific article

A particle swarm based hybrid system for imbalanced medical data sampling

scientific article published on 3 December 2009

An improved Akt reporter reveals intra- and inter-cellular heterogeneity and oscillations in signal transduction.

scientific article published on 29 June 2017

An integrative systems genetic analysis of mammalian lipid metabolism

scientific article published on 27 February 2019

Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis

scientific article published on 24 December 2019

CNOT3-Dependent mRNA Deadenylation Safeguards the Pluripotent State

scientific article published on 08 October 2016

Confronting two-pair primer design for enzyme-free SNP genotyping based on a genetic algorithm.

scientific article

Data Independent Acquisition Proteomic Analysis Can Discriminate between Actinic Keratosis, Bowen's Disease, and Cutaneous Squamous Cell Carcinoma

scientific article published on 27 June 2019

Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway

scientific article

Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal

scientific article

Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates.

scientific article

Global redox proteome and phosphoproteome analysis reveals redox switch in Akt

scientific article published on 02 December 2019

Hierarchical kernel mixture models for the prediction of AIDS disease progression using HIV structural gp120 profiles.

scientific article

Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors.

scientific article

Integrated glycoproteomics identifies a role of N-glycosylation and galectin-1 on myogenesis and muscle development

scientific article published on 16 September 2020

Intragenic Enhancers Attenuate Host Gene Expression.

scientific article

Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data

scientific article

NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region

scientific article published on 11 July 2019

NoisyGOA: Noisy GO annotations prediction using taxonomic and semantic similarity.

scientific article published on 13 September 2016

Protocol for the processing and downstream analysis of phosphoproteomic data with PhosR

scientific article published on 05 June 2021

QCMAP: An Interactive Web-Tool for Performance Diagnosis and Prediction of LC-MS Systems

scientific article published on 13 June 2019

Sample Subset Optimization Techniques for Imbalanced and Ensemble Learning Problems in Bioinformatics Applications

scientific article published on 30 September 2013

Temporal ordering of omics and multiomic events inferred from time-series data

scientific article published on 16 July 2020

Unraveling Kinase Activation Dynamics Using Kinase-Substrate Relationships from Temporal Large-Scale Phosphoproteomics Studies

scientific article

mTORC1 Is a Major Regulatory Node in the FGF21 Signaling Network in Adipocytes.

scientific article published in September 2016

scClassify: sample size estimation and multiscale classification of cells using single and multiple reference

scientific article published on 01 June 2020

scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction

scientific article published in 2022

scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets

scientific article published on 26 April 2019

scREMOTE: Using multimodal single cell data to predict regulatory gene relationships and to build a computational cell reprogramming model

scientific article published on 15 March 2022

scReClassify: post hoc cell type classification of single-cell rNA-seq data

scientific article published on 24 December 2019

List of works by Pengyi Yang

A benchmark study of simulation methods for single-cell RNA sequencing data

A hierarchical approach to removal of unwanted variation for large-scale metabolomics data

A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data

A particle swarm based hybrid system for imbalanced medical data sampling

An improved Akt reporter reveals intra- and inter-cellular heterogeneity and oscillations in signal transduction.

An integrative systems genetic analysis of mammalian lipid metabolism

Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis

CNOT3-Dependent mRNA Deadenylation Safeguards the Pluripotent State

Confronting two-pair primer design for enzyme-free SNP genotyping based on a genetic algorithm.

Data Independent Acquisition Proteomic Analysis Can Discriminate between Actinic Keratosis, Bowen's Disease, and Cutaneous Squamous Cell Carcinoma

Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway

Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal

Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates.

Global redox proteome and phosphoproteome analysis reveals redox switch in Akt

Hierarchical kernel mixture models for the prediction of AIDS disease progression using HIV structural gp120 profiles.

Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors.

Integrated glycoproteomics identifies a role of N-glycosylation and galectin-1 on myogenesis and muscle development

Intragenic Enhancers Attenuate Host Gene Expression.

Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data

NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region

NoisyGOA: Noisy GO annotations prediction using taxonomic and semantic similarity.

Protocol for the processing and downstream analysis of phosphoproteomic data with PhosR

QCMAP: An Interactive Web-Tool for Performance Diagnosis and Prediction of LC-MS Systems

Sample Subset Optimization Techniques for Imbalanced and Ensemble Learning Problems in Bioinformatics Applications

Temporal ordering of omics and multiomic events inferred from time-series data

Unraveling Kinase Activation Dynamics Using Kinase-Substrate Relationships from Temporal Large-Scale Phosphoproteomics Studies

mTORC1 Is a Major Regulatory Node in the FGF21 Signaling Network in Adipocytes.

scClassify: sample size estimation and multiscale classification of cells using single and multiple reference

scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction

scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets

scREMOTE: Using multimodal single cell data to predict regulatory gene relationships and to build a computational cell reprogramming model

scReClassify: post hoc cell type classification of single-cell rNA-seq data