Description: Description: Description: Description: D:\Work\lab meeting\head.jpg

 

 

 

 

 

 

 

 

 

 

 

 

Group Meetings



2020/04/14

Jian Zou

Evaluation of Adaptive Fisher and AW Fisher

2020/04/07

Xiangning Xue

Semi-supervised learning on sount data

2020/03/31

Yujia Li

AW-Fisher and adaptive Fisher method in multivariate outcome application.

2020/03/23

Wei Zong

Literature review: Multi-tissue Multi-individual Clustering Using Tensor Decomposition.

2020/03/16

Yusi Fang

Combining P-values for Dependent Tests with Heavy-tailed Distributions.

2020/03/20

Peng Liu

Outcome-guided clustering with updated robust regression.

2020/03/03

Jian Zou

Literature review: Cross-study Replicability in Cluster Analysis.

2020/02/25

Xiangning Xue

Literature review: Consensus Subtyping in Colorectal Cancer.

2020/02/18

Yujia Li

Literature review: Gene Regulartory Network.

2020/02/11

Wei Zong

Literature review: Low-rank Tensor Constrained Multiview Subspace Clustering.

2020/02/04

Yusi Fang

Literature review: Standardized Partial Sums and Products of P-values & Tests Alternative to Higher Criticism for High-dimensional Means under Sparsity and Column-wise Dependence.

2020/01/21

Peng Liu

Literature review: Survival-based Bayesian Clustering.

2020/01/14

Yujia Li

Literature review: Bipartite Tight Spectral Clustering(BiTSC) for Identifying Conserved Gene Co-clusters in Two Species.

2019/12/13

Wei Zong

Literature review: Multi-view Clustering Methods.

2019/12/06

Yusi Fang

Detection of sparse, weak and heterogeneous signals.

2019/11/22

Peng Liu

Literature Review: Methods to integrate high-throughput omics data (Tensor regression).

2019/11/01

Wei Zong

Literature Review: Pathway analysis and comaprative studies.

2019/10/18

Yujia Li

Literature Review: Screening methods.

2019/10/11

Yusi Fang

Literature Review: Higher criticism for detecting sparse heterogeneous mixtures.

2019/10/04

Peng Liu

Literature Review: ADMM algorithm

2019/09/27

Wei Zong

Robust Order-based Machine Learning (ROML)

2019/09/20

Yujia Li

Literature Review: Semi-supervised learning (penalized Gaussian mixture model, Self-training, Co-training)

2019/09/13

Yusi Fang

Meta-analysis method by combining m-top p-values

2019/09/06

Peng Liu

Outcome guided disease subtyping for high dimensional omics data

2019/4/11, 2019/4/25, 2019/5/9

Department of Biostatistics

"A world beyond p < .05": discussion and literature review of papers relating to the use of the p-value, as well as potential alternatives to the p-value in scientific research.

2019/3/28

Yusi Fang

Literature Review: BayICE

2019/3/21

Tanbin Rahman

Sparse Negative binomial classifier for RNA-seq data with covariate adjustment

2019/3/7

Wei Zong

Literature Review: Meta-analysis of the human brain transcriptome identifies heterogeneity across human AD coexpression modules robust to sample collection and methodological approach

2019/2/28

Li Zhu

Literature Review: Semi-supervised clustering methods

2019/2/21

Peng Liu

Disease subtyping

2019/2/14

Kelly Cahill

Literature Review of existing TSP + machine learning methods

2019/2/7

Yujia Li

Simultaneous estimation of number of clusters and feature sparsity in clustering high dimensional data using resampling methodsoplet-based single cell transcriptomic data from population studies

2019/1/31

Yusi Fang

Literature Review: DIMM-SC: A Dirichlet mixture model for clustering droplet-based single cell transcriptomic data & BAMM-SC: A Bayesian mixture model for clustering droplet-based single cell transcriptomic data from population studies

2019/1/24

Tanbin Rahman

Sparse Negative binomial classifier for RNA-seq data with covariate adjustment

2018/12/4

Kelly Cahill

Nonparametric feature selection and robust classification for accurate inter-study prediction of categorical and continuous outcomes.

2018/11/27

Huang Lin

Introduction to Microbiome Analysis

2018/11/13

Tanbin Rahman

Sparse Classification for RNA seq data with covariate adjustment

2018/10/23

Yujia Li

Bayesian model based clustering with feature selection

2018/10/23

Yusi Fang

Semi-supervised clustering for single cell RNAseq data

2018/10/9

Li Zhu

Bayesian clustering with multi-layer overlapping group structure

2018/10/2

Peng Liu

MethylSeqDesign: A framework for Methyl-Seq genome-wide power calculation and study design issues

2018/9/25

Kelly Cahill

A simulation study for binary and multi-class prediction using top scoring pairs in conjunction with random forest trees

2018/9/18

Yujia Li

Simultaneous estimation of number of clusters and feature selection in clustering high-dimensional data using resampling methods.

2018/9/11

YuSi Fang

Apply adaptive weighted fisher statistic in testing association between clinical outcomes and biomarker.

2018/9/4

Lu, Han-jun

Bayesian inference in feature selection and clustering for RNA sequence count data.

2018/9/4

Huang, Hsin-En

sparse Negative Binomial Linear Discriminant Analysis for RNAseq data.

2018/8/28

Tanbin Rahman

Sparse Negative Binomial model-based clustering for RNA-sequence count data.

2018/8/21

Li Zhu

Bayesian indicator variable selection model for multi-layer overlapping groups in multi-omics application.

2018/8/14

Peng Liu

AW Fisher method and extensions.

2018/8/7

Kelly Cahill

Top Scoring Pairs + Machine learning methods for binary classification.

2018/1/16

George C. Tseng

Lab overview.

2017/12/11

Tanbin Rahman

Clustering for Count data with application to RNA sequence data.

2017/11/28

Peng Liu

Apply AW Fisher method in testing association between clinical outcomes and biomarkers.. Download (Protected file for internal use)

2017/11/21

Tianzhou (Charles) Ma

Job talk practice.

2017/11/14

Shyamal D Peddada

Rhythmic signals related to human microbiome.

2017/11/7

Kelly Cahill

Top scoring pairs for feature selection in machine learning and applications to cancer outcome prediction

2017/11/1

Li Zhu

Introduction of basic knowledge of deep neural network

2017/10/24

Tianzhou (Charles) Ma

Overview of diffusion MRI (dMRI) projects

2017/10/17

Tanbin Rahman

Model based Clustering for RNA sequence data, Download (Protected file for internal use)

2017/9/26

Peng Liu

Exome sequencing analysis Download (Protected file for internal use)

2017/9/19

Kelly Cahill

Nonparametric feature selection and robust classification for accurate inter-study prediction of binary outcomes.

2017/7/20

An-shun Tai

Zero-inflated negative binomial mixed regression for detecting transcriptional changes in single-cell RNA sequencing data.

2017/4/28

Zhiguang (Caleb) Huo

Adaptively weighted Fisher's method.

2017/4/21

Tianzhou (Charles) Ma

Meta-screening and meta-regularization.

2017/4/14

Li Zhu

Extend Bayesian variable selection method for multi-layer overlapping groups to clustering.

2017/4/7

Shuchang (Silvia) Liu

Dissertation defense Rehearsal: Genomic integrative analysis to improve fusion transcript detection, liquid association and biclustering

2017/3/31

Tanbin Rahman

Clustering of Count data with application to RNA sequence data

2017/3/24

Zhou(Ark) Fang

Integrative Multi-Omics Analysis - A Bayesian Framework Inspired by iBAG with Missingness Handling

2017/3/17

An-shun Tai

Inferring evolution structure based on copy number aberration from head and neck cancer via two-way mixture Poisson model

2017/3/3

Peng Liu

Power Calculation for DNA methylation study design and analysis Download (Protected file for internal use)

2017/2/17

Kelly Cahill

A robust model for molecular age prediction using top scoring pairs Download (Protected file for internal use)

2017/2/3

Chien-Wei (Masaki) Lin

Job Talk Practice

2017/1/20

Zhiguang Huo(Caleb)

Meta-analytic and integrative framework for sparse K-means to identify disease subtypes

2016/12/6

Chien-Wei Lin (Masaki)

Proposal Practice

2016/11/1

Shuchang Liu (Silvia)

Horizontal meta-analysis to detect biclusters by plaid model

2016/10/25

Zhou Fang (Ark)

Bayesian Framework for Integrative Omics Analysis with Missing Covariates Data Download (Protected file for internal use)

2016/10/11

Tianzhou Ma (Charles)

Identification of stable functional modules from GGM-constructed network (mainly review) Download (Protected file for internal use)

2016/10/4

Tanbin Rahman

Cross-species Gene Expression Analysis:Resemblance between Human and mice models Download (Protected file for internal use)

2016/9/27

Zhiguang Huo (Caleb)

Integrative Sparse K-means for disease subtype discovery Download (Protected file for internal use)

2016/9/13

Chien-Wei Lin (Masaki)

SeqDesign: A framework for RNA-Seq genome-wide power calculation and experimental design issues Download (Protected file for internal use)

2016/8/26

Anche Kuo

Shiny tutorial and MetaOmics coding structure Download (Protected file for internal use)

2016/8/19

Li Zhu

Bayesian hierarchical model for multi-level overlapping group structure (MOG) Download (Protected file for internal use)

2016/8/12

Zhou Fang (Ark)

Bayesian Framework for Integrative Omics Analysis with Missing Covariates Data Download (Protected file for internal use)

2016/8/5

Tianzhou Ma (Charles)

Bayesian latent variable model for integrating microarray and RNA-seq transcriptomic data Download (Protected file for internal use)

2016/7/22

Tanbin Rahman

Cross-species Gene Expression Analysis: Resemblance between Human and mice models Download (Protected file for internal use)

2016/7/15

Zhiguang Huo (Caleb)

Bayesian non-parametric latent hierarchical model for transcriptomic meta-analysis to detect biomarkers with clustered meta-patterns of differential expression signals Download (Protected file for internal use)

2016/3/1

Li Zhu

Bayesian sparse group lasso Download (Protected file for internal use)

2016/2/23

Zhou Fang (Ark)

Bayesian Framework for Integrative Omics Analysis with Missing Covariates Data Download (Protected file for internal use)

2016/2/16

Tianzhou Ma (Charles)

Cross-platform meta-analysis of microarray and RNA-seq Download (Protected file for internal use)

2016/2/9

Shuchang Liu (Silvia)

Horizontal meta-analysis to detect biclusters by plaid model Download (Protected file for internal use)

2016/2/2

Tanbin Rahman

Cross-species Gene Expression Analysis:Resemblance between Human and mice models Download (Protected file for internal use)

2016/1/26

Lin Wang

Meta analysis for liquid association Download (Protected file for internal use)

2016/1/19

Zhiguang Huo (Caleb)

Biomarker categorization and fast computing of adaptively weighted Fisher's method for meta-analysis in omics applications Download (Protected file for internal use)

2016/1/12

Chien-Wei Lin (Masaki)

Genetic Modulation of Brain Molecular Aging Download (Protected file for internal use)

2015/12/11 (Fri)

Li Zhu

Bayesian group lasso and approximate inference Download (Protected file for internal use)

2015/11/20 (Fri)

Zhou Fang (Ark)

Hidden Markov Model(HMM) and Sequential Importance Sampling(SIS) for imputation, phasing, and genotype calling Download (Protected file for internal use)

2015/11/13 (Fri)

Tianzhou Ma (Charles)

Bayesian cross-platform meta-analysis of microarray and RNA-seq Download (Protected file for internal use)

2015/11/6 (Fri)

Shuchang Liu (Silvia)

Targeted fusion breakpoint detection from WGS data and duplicate reads detection from NGS data Download (Protected file for internal use)

2015/10/30 (Fri)

Zhiguang Huo (Caleb)

Integrative Sparse K-means for disease subtype discovery Download (Protected file for internal use)

2015/10/23 (Fri)

Chien-Wei Lin (Masaki)

Genetic Modulation of Brain Molecular Aging Download (Protected file for internal use)

2015/10/9 (Fri)

Li Zhu

Meta-analysis Framework for Differential Coexpression Module Detection (MetDiffNetwork) Download (Protected file for internal use)

2015/10/2 (Fri)

Zhou Fang (Ark)

A Bayesian Framework for Two Way Integrative Analysis on Two Tissue Asthma Data Download (Protected file for internal use)

2015/09/25 (Fri)

Tianzhou Ma (Charles)

Integrative analysis of multi-omics data across multiple cancer types Download (Protected file for internal use)

2015/09/18 (Fri)

Shuchang Liu (Silvia)

Extending plaid model to detect biclusters in horizontal meta-analysis framework Download (Protected file for internal use)

2015/09/11 (Fri)

Zhiguang Huo (Caleb)

Single Cell Methylation Download (Protected file for internal use)

2015/09/04 (Fri)

Chien-Wei Lin (Masaki)

Overview of the Integration Between Neuroimaging and Genetics Download (Protected file for internal use)

2015/08/25 (Tue)

Group Project Overview

Adaptive weight Fisher and 12 other presentations Download (Protected file for internal use)

2015/04/23 (Thu)

Qi Yan

Region-based Association Tests for DNA Methylation Data

2015/04/10 (Fri)

Zhiguang Huo

Bayesian Latent model for omics meta analysis for idientifying consensus and study-specific biomarkers Download (Protected file for internal use)

2015/03/27 (Fri)

Tianzhou Ma

Bayesian hierarchical model for the meta-analysis of RNAseq Download (Protected file for internal use)

2015/03/20 (Fri)

Chien-Wei Lin & SungHwan Kim

1. Consensus and differential GO pathway analysis and visualization when multiple transcriptomic studies or conditions are jointly analyzed, 2. A meta-analysis framework for principal component analysis Download (Protected file for internal use)

2015/03/03 (Tue)

Qi Yan & Ting Wang

1. Rare-Variant Kernel Machine Test for Longitudinal Data for Population and Family Samples, 2. A fast package of constructing conditional Gaussian graphical model for a large number of variables

2015/02/27 (Fri)

Zhou Fang(Ark)

Plaid Model and Its Extension for MetaBiclustering Download (Protected file for internal use)

2015/02/06 (Fri)

Chien-Wei Lin

Consensus and differential GO pathway analysis and visualization when multiple transcriptomic studies or conditions are jointly analyzed Download (Protected file for internal use)

2015/01/30 (Fri)

Shuchang Liu

RNA methylation analysis by RNA-seq and m6A-seq Download (Protected file for internal use)

2015/01/23 (Fri)

Tianzhou Ma & Zhiguang Huo

1. Bayesian hierarchical model for the meta-analysis of RNAseq, 2.Bayesian method for differential expressed genes of meta analysis Download (Protected file for internal use)

2015/01/16 (Fri)

George Tseng

Annual lab overview and future directions Download (Protected file for internal use)

2014/12/15 (Mon)

Ting Wang & Qi Yan

(1) An evaluation of Normalization Approaches for Illumina Infinium 450K Methylation Data (2) Effects of sequencing errors on family-based association tests for rare variants

2014/12/09 (Tue)

Tianzhou Ma

Bayesian hierarchical model for the meta-analysis of RNAseq Download (Protected file for internal use)

2014/12/02 (Tue)

Zhou Fang (Ark)

Sparse K-means clustering and Gaussian Mixture Model (GMM) Download (Protected file for internal use)

2014/11/25 (Tue)

Rui Chen

Comparative study of two Meta-gene-clustering approaches for co-regulated expression identification Download (Protected file for internal use)

2014/11/18 (Tue)

Shuchang Liu & Chien-Wei Lin

Joint group meeting with Wei Chen's group @GSPH Download (Protected file for internal use)

2014/11/11 (Tue)

Zhiguang Huo

Bayesian method for differential expressed genes of meta analysis Download (Protected file for internal use)

2014/11/04 (Tue)

SungHwan Kim

A meta-analysis framework for sparse principal component analysis Download (Protected file for internal use)

2014/10/27 (Mon)

Qi Yan & Yi Liu

(1) Kernel Machine Regression for Multivariate Quantitative Phenotype in Family Samples (2) Comparison study of multivariate survival models

2014/10/21 (Tue)

Tianzhou Ma

How much can mouse models predict human disease on a molecular basis: from differential expression to pathway analysis Download (Protected file for internal use)

2014/10/07 (Tue)

Chien-Wei Lin

SeqDEsign: a framework for Genome-wide power calculation and design issues in RNA-Seq Experiment Download (Protected file for internal use)

2014/09/30 (Tue)

Rui Chen

Comparative study of two Meta-gene-clustering approaches for co-regulated expression identification. Download (Protected file for internal use)

2014/09/23 (Tue)

Shuchang Liu

A comprehensive evaluation of fusion transcript detection algorithms in pair-end RNA-Seq data Download (Protected file for internal use)

2014/09/16 (Tue)

Zhiguang Huo & SungHwan Kim

Joint group meeting with Wei Chen's group @GSPH Download (Protected file for internal use)

2014/09/02 (Tue)

Tianzhou Ma

Unified fixed and random effect model and their adaptive-weighted versions for the meta-analysis of RNAseq Download (Protected file for internal use)

2014/04/24

Chien-Wei Lin

Thresholding adaptive weighting methods for identifying concordant differentially expressed genes in omics meta-analysis Download (Protected file for internal use)

2014/04/17

Serena Liao

SeqDEsign: A novel power calculation method for candidate marker detection in RNA-seq experiment Download (Protected file for internal use)

2014/04/03

Rui Chen

Proposal rehearsal Download (Protected file for internal use)

2014/03/27

Lun-Ching Chang

Job talk rehearsal

2014/03/20

Zhiguang Huo

Sparse Gaussian Mixture Model Download (Protected file for internal use)

2014/02/27

ENAR rehearsal

2014/02/20

Cho-Yi Chen

Analysis of MicroRNA Regulatory Network and 3'UTRome Download (Protected file for internal use)

2014/02/13

Shaowu Tang

Job talk rehearsal Download (Protected file for internal use)

2014/02/06

Ding Ying

Job talk rehearsal Download (Protected file for internal use)

2014/01/30

Lun-Ching Chang

Analysis of Family-based Sequence Data Download (Protected file for internal use)

2014/01/16

SungHwan Kim

Group structured integrative clustering for identifying coherent samples in inter-related multiple genomic data sets Download (Protected file for internal use)

2014/01/09

George Tseng

Annual lab overview Download (Protected file for internal use)

2013/12/09

Ding Ying

Meta-network analysis for gene coexpression

2013/11/25

Rui Chen

ChIP-seq Meta-Caller: An assembly method to combine multiple ChIP-seq peak callers to identify and reprioritize the peaks

2013/11/18

Serena Liao

A mixture model approach for sample size and power calculation in RNAseq data

2013/11/11

Shaowu Tang

Imputation of truncated p-values for meta-analysis methods and its genomic application

2013/11/04

Chien-Wei Lin

An interactive visualization tool for biological pathway with an emphasis on overlapping structure

2013/10/28

Zhiguang Huo

Meta-analysis sparse K-means framework for disease subtype discovery when combining multiple transcriptomic studies

2013/10/21

Lun-Ching Chang

Analysis of Family-based Sequence Data

2013/9/9

SungHwan Kim

Double-penalized integrative clustering for identifying stable and coherent samples in multiple genomic data sets

2013/8/26

Ding Ying

Dissertation Rehearsal

2013/8/20

Rui Chen

Somatic Point Mutation Detection on Prostate Cancer Samples

2013/8/13

Serena Liao

Missing value imputation in high dimensional phenome data

2013/7/30

Shaowu Tang

2013/3/5

Xiaojing Zheng

A review of my research work

2013/2/26

Zhiguang Huo

Meta-analysis framework of sparse K-means for disease subtype discovery

2013/2/19

Lun-Ching Chang

Molecular brain aging and genetic modulation

2013/2/12

SungHwan Kim

Integrative Phenotyping Framework (iPF): Integration of Phenomic and Genomic Data

2013/2/5

Ying Ding

Bias correctioin in the selection of minimal-error classifier from many machine learningmodels.

2013/1/29

Wei Chen

A Sketch of My Methodological and Applied Genetic Research

2013/1/22

Rui Chen

Meta-ChIP-seq Project in Comparing and Combining Peak Callers

2013/1/15

George C. Tseng

Annal lab summary and Plan for research

2012/12/11

Daniel E. Weeks

Practical Challenges in Applied Statistical Genetics Research

2012/12/04

Shaowu Tang

Investigation on adaptively weighted evidence aggregation meta-analysis methods

2012/11/27

Cancel Group Meeting

2012/11/20

Xingbin Wang

Data Adaptively Weighted Association Test Method for Rare Variant Detection

2012/11/13

Eleanor Feingold

A much more informal than it looks talk on my research

2012/11/06

Serena Liao

Methylation events in aging as drivers of breast cancer tumorgensis

2012/10/30

Hurricane Sandy Break

2012/10/23

Zhiguang Huo

Framework of Meta Sparse KMeans

2012/10/16

Lun-Ching Chang

Molecular Evidence for a Dimensional Basis of Depression

2012/10/02

Sunghwan Kim

A meta-analysis framework for principal component analysis: with applications to combining multiple transcriptomic studies 

2012/09/25

Kui Shen

Epigenomic Regulation of Gene Expression in Diet Induced Obesity

2012/09/18

Ying Ding

Bias correction in the selection of minimal-error classifier from many machine learning models. 

2012/09/11

Rui Chen

NGS analysis on Methylation and RNA-seq Data of Prostate Cancer

2012/08/24

Shaowu

Investigations on the bias of minimal error rate induced by optimal classifier selection algorithm in microarray data analysis (theoretical results)

2012/08/17

Serena Liao

Missing value imputation in phenome data

2012/04/16

Lun-Ching

Molecular brain aging: genetic modulation and functional outcomes

2012/04/09

Sunghwan

TSP with Housekeeping Gene

2012/04/02

 

ENAR meeting 2012 (Washington DC)

2012/03/26

 

ENAR rehearsal

2012/03/19

 

CMU statistics seminar

2012/03/12

Ying Ding

Meta-analysis for combining multiple

relevant regulatory networks

2012/02/27

Chi Song

Robust Meta-analysis Methods for Genomic Studies

2012/02/13

Shaowu

Imputation of truncated p-values for order statistics meta-analysis methods

2012/02/06

Ge Liao

Missing value imputation for phenome data

2012/01/30

Lun-Ching

Comprehensive comparative microarray meta-analysis methods

2012/01/23

Sunghwan

TSP with Housekeeping Gene

2012/01/09

George

Project review by person

2011/12/02

George

Intro of academic career

2011/11/18

Ying Ding

Regularity network analysis by meta-analysis of multiple transcriptomic studies in major depressive disorder

2011/11/11

Chi Song

Logistic Mixture Model for Meta-analysis

2011/10/14

Shaowu

Combining p-values by Stouffer and Fisher's methods when p-values censored in partial studies

2011/09/30

Ge Liao

Extending K-nearest neighbor imputation to phenotype data

2011/09/23

Lun-Ching

Comparative study of microarray meta-analysis

2011/09/16

Ying Ding

Principles and challenges of genomewide DNA methylation analysis

2011/09/09

Chi Song

IPOD and Module-based MDS

2011/09/02

Shaowu

Combining p-values by Stouffer and Fisher's methods when p-values censored in partial studies

2011/08/22

Ge Liao

Extend K-Nearest Neighbor imputation to phenotype data

2011/08/15

Lun-Ching

Comparative study of microarray meta-analysis

2011/03/28

Lun-Ching

MDD project

2011/03/21

Shaowu

Extending Fisher?s method for meta-analysis when partial p-value information is available

2011/02/28

Don

Meta Sparse PCA

2011/02/21

Chuck

Paper review

2011/02/14

Shaowu

Extending Fisher?s method for meta-analysis when partial p-value information is available

2011/02/07

Xingbin

Meta-regression

2011/01/31

Lun-Ching

LOHAS paper

2011/01/24

Don

Meta-PCA

2011/01/17

Dr. George

Project overview and looking forward to 2011

2010/12/20

Chuck

Paper review: An integrated analysis of molecular aberrations in NCI-60 cell lines. BMC bioinfo 2010

2010/12/06

Lun-Ching

Synergizing transcriptome and genome-wide association studies in depression and other neuropsychiatric disorders

2010/11/29

No meeting today: Thanksgiving break

2010/11/22

Xingbin

Rehearsal of the proposal

2010/11/12

Don

Statistical issues in combining multiple genomic studies: quality assessment, dimension reduction and integration of transcriptomic and phenomic data

2010/11/8

Chuck

Paper review: Next-generation genomic an integrative approach

2010/11/1

Xingbin

Two stage Meta-Analysis for MDD

2010/10/25

Lun-Ching

Synergizing transcriptome and genome-wide association studies in depression and other neuropsychiatric disorders

2010/10/18

Don

Integrative quality control for genomic microarray analysis

2010/10/03

Chuck

r-th ordered P-value for meta-analysis

2010/09/27

Group meeting

Discuss meat-analysis data sets

2010/09/20

Xingbin

MDD data sets

2010/09/13

Don

Weighted meta-analysis

2010/08/30

Chuck

Rth rank

2010/08/23

Xingbin

Meta-analysis on Depression microarray studies

2010/08/16

Don

Meta-analysis: pathway weighting method

2010/08/09

Xingbin

Paper review

2010/07/12

Don

Meta-cluster

2010/06/30

Xingbin

Meta-analysis: Random intercept model

2010/03/24

Don

Meta PCA

2010/03/17

Chuck

Survival analysis project and method review

2010/02/24

Xingbin

EVC based on Rank correlation

2010/02/17

Don

Clustering of variables

2010/02/03

Chuck

Paper review

2010/01/27

Xingbin

Application of EVC in real data sets

2010/01/20

Don

?/span>Meta FDA

2010/01/13

Chuck

Rth rank method

2010/01/06

George

Review of projects and papers

2009/12/14

Xingbin

Meta-analysis on Depression (Human and mouse)data sets

2009/11/30

Don

Meta FDA(II)

2009/11/23

Chuck

An analysis of cancer data

2009/11/16

Xingbin

Application of EVC

2009/11/09

Jiawei

Partial least square?Theorem and Algorithm

2009/11/02

Don

Meta-FDA

2009/10/19

Chuck

The next generation

2009/10/05

Xingbin

Asymptotic property of EVC estimator

2009/09/28

Don

Meta-analysis for integrated data exploratory tools

2009/08/31

Chuck

Generalized Singular Value Decomposition (GSVD)

2009/08/27

Xingbin

EVC: Inferring the True correlation of Cross-Species Microarray Data

2009/08/20

Don

Meta-Clustering & Meta-PCA

2009/08/13

Kui

Defense rehearsal

2009/07/30

Chuck

Cell Cycle Paper Review

2009/07/23

Kui

Defense rehearsal

2009/07/16

Xingbin

ABO: Asymptotically Bahadur Optimal Property of OW method

2009/07/09

Shuya

Defense rehearsal

2009/6/11

Sunghee

Defense rehearsal

2009/6/4

Shuya

6/4 R PACKAGES FOR DATA QUALITY EVALUATION AND RETRIEVAL OF MICROARRY STUDIES

2009/5/28

Chuck

Paper review:

Sunita R. Setlur et al. 2007

Sridhar Ramaswamy et al. 2002

2009/5/14

Kui

Combining multiple microarray studies for improved pathway analysis

2009/5/7

Xingbin

Asymtotically Optimal Methods of Combining Tests

2009/4/28

Sunghee

Effects of missing value imputation on down-stream analyses in microarray data

2009/4/21

Chuck

GSEA algorithm

2009/4/13

Shuya

R function for merging microarray data sets and Data quality control

2009/3/23

Kui

Combining multiple microarray studies for improved pathway analysis

2009/3/16

Xingbin

Asymtotically Optimal Methods of Combining Tests

2009/3/2

Sunghee

The effects of missing value imputation on down-stream analyses of microarray data

2009/2/2

Chuck

Tight Clustering R package

2009/1/26

Shuya

Data collection package and biomarkers detection for a real cancer data.

2009/1/12

Kui

Combining multiple microarray studies for improved pathway analysis

2009/1/5

George

Overview the projects and research direction

2008/12/15

Xingbin

Estimating the true correlation in a contaminated bivariate Gaussian model: via extreme value correlation

2008/12/8

Sunghee

Rehearsal for proposal

2008/11/17

Kui

Combining multiple microarray studies for improved pathway analysis

2008/11/10

Shuya

Review paper:
Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progrssion Rhodes DR et al.(2004)PNAS.
Detecting common gene expression pattens in multiple cancer outcome entities. Yang X et al.(2005)Biomedical Microdevices.

2008/11/03

Chuck

Rearranged Ions in Mass Spectrometry Research

2008/10/27

Sunghee

Effects of missing imputation on various down-stream analyses in microarray experiments

2008/10/20

Xingbin

Estimating the true correlation in a contaminated bivariate Gussian model via extreme value correlation

2008/10/06

Zhibao

Dimension Reduction and Robust Classification Models in the Disease Prediction by Genomic and Cell-based Assays

2008/09/29

Kui

Review paper:
Meta- and Gene set analysis of stomach cancer gene expession data,Seon-Young Kim et al., Mol. Cells, Vol.24, No.2, p.200-209

2008/09/22

Shuya

Biomarker Detection methods when combining multiple multi-class mircoarrays studies

2008/09/15

Xingbin

Estimating the true correlation in a contaminated bivariate Gaussian model:via extreme value correlation

2008/09/08

Sunghee

The effects on identifying the significant genes to various MVs imputation methods

2008/09/02

Kui

Rehearsal for proposal

08/8/25

Kui

Combining multiple microarray studies for improved pathway analysis

08/8/18

Shuya

Identifying Biomarkers of Concordant Patterns in the Meta-Analylsis of multilple multi-class microarray studies

08/8/11

Sunghee

The effects on identifying the significant genes to various missing values(MVs) imputation methods

08/8/05

Xingbin

Estimating the true correlation in a contaminated bivariate Gaussian model:via extreme value correlation

08/7/28

Zhibao

MBP Project Update

08/6/30

Kui

Identifying alternative pathway using Fisher Exact Test

08/6/23

Shuya

Review paper:
Regularized biomarker selection in mircroarray meta-analysis,
Shuangge Ma et al,Technical Report No.383

08/6/09

Sunghee

The effects on identifying the significant genes to various missing values(MVs) imputation methods

08/5/19

Zhibao

Module-based prediction in microarray data(MBP)

08/5/12

Kui

Module Enrichment Meta-analysis of Microarray Data

08/5/5

Shuya

Identifying biomarkers of concordant correlated patterns across microarray studies

08/4/21

Sunghee

Review paper:
DNA microarray data imputation and significance analysis of differential expression, Jornsten et al, Bioinformatics, p.4155-4161.

08/4/14

Zhibao

Rehearsal for proposal

08/4/07

Chunrong

Review paper:
Metagene projection for cross-platform, cross species characterization of global transcriptional states,Tamayo et al, PNAS, p.5959-5964.

08/3/24

NIH meeting

Group meeting cancelled

08/3/17

ENAR

Group meeting cancelled

08/3/10

Spring break

Group meeting cancelled

08/3/03

Jia

Review paper:
Pearson's Test in a Large Scale Multiple Meta-Anlysis, Art B.Owen

08/2/25

Shuya

1.Identifying genes with correlated patterns across studies
2.Review workshop from HBLS Bioinformatics:Protein Information Hubs

08/2/18

Kui

A tutorial for making a R package in Windows

08/2/11

Zhibao

Module based robust prediction

08/2/04

Sunghee

Estimating the true correlation in a contaminated bivariate Gaussian model : via extreme value correlation

08/1/28

Kui

Multi-resolution classification

07/11/20

Chunrong
Jia

rehearsal for proposals

07/11/13

Shuya

identifying correlated genes across studies

07/11/6

Zhibao

module-based prediction model

07/10/30

Jia

Meta-analysis of microarray data

07/10/23

Chunrong

cross-platform prediction

07/10/16

Sunghee

Correlation of extreme values

07/10/2

Kui

Multi-resolution clustering

07/9/25

Shuya

Review paper:
Optimized cross-study analysis of microarray based predictors,X.Zhong et al.

07/9/18

Zhibao

module-based prediction model

07/9/11

Jia

meta-analysis in microarray

07/9/4

Chunrong

cross-dataset prediction and improved DE gene detection method

07/8/27

Sunghee

extreme value correlation and identify correlated genes across species

07/8/20

George

evolution of gene identifiers and issues in gene matching across data sets

07/8/13

Kui Shen

improved tight clustering/multi-resolution clustering

07/8/6

Sunghee

extreme value correlation and identify correlated genes across species

07/7/16

Jia Li

meta-analysis in microarray

07/7/9

Zhibao

robust prediction in microarray

07/7/2

Chunrong

cross-dataset prediction in microarray

07/5/18

Sunghee

The connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes and Disease. Science. 2006

07/5/11

Chunrong

From signature to models: understanding cancer using microarrays. Nature Genetics. 2005

07/5/4

Jia

A module map showing conditional activity of expression modules in cancer. Nature Genetics. 2004

07/4/13

Sunghee

analysis on human and mouse depression; simulation on extreme correlation

07/4/6

Zhibao

a robust prediction method

07/3/30

Joshua

preparing microarray data packages and annotations in Bioconductor

07/3/23

Jia

update on meta-analysis project

07/2/16

Joshua

Review paper: Bayesian models for pooling microarray studies with multiple sources of replications.

07/2/9

George

Quantile map: visualizing and summarizing patterns of multiple distributions with Fisher information and empirical Bayes.

07/2/2

Chunrong

Review paper: Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes.

07/1/26

Sunghee

Review paper: Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression.

07/1/19

Jia

Review paper: Statistical issues and methods for meta-analysis of microarray data: a case study in prostate cancer.
Meta-analysis ofmicroarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer.

06/12/18

Jia
Sunghee

Review NBT MAQC paper: Using RNA sample titrations to assess microarray platform performance and normalization techniques.
review NBT MAQC paper: Evaluation of DNA microarray results with quantitative gene expression platforms.

06/11/27

George

Statistical integrative analysis of multiple expression profiles
review NAR paper (Chunrong): Evaluation of gene expression measurements from commercial microarray platforms.

06/11/20

Zhibao

update on KNN.e imputation
review NBT MAQC paper (George): The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

06/11/06

Jia

gene selection in classification of microarray data

06/10/30

Sunghee

Metastasis of ovarian and endometrial cancer in expression profiles

06/10/16

Chunrong

Cross-organ classification analysis on expression profiles of liver and prostate cancer

06/10/02

George

Selection of missing value imputation methods in microarray

06/09/25

Jia

Increasingly exhaustive gene/covariate selection

06/09/18

Chunrong

KNN-SAM

06/09/11

Zhibao

Correlation-based KNN in missing value imputation

06/08/30

Sunghee

Analysis of human depression data

06/08/03

Chunrong

Meta-analysis on prostate and lung cancer data

06/07/13

George

Summary of all projects. Penalized and weighted K-means.