Microarrays

PDF

Regulatory Motif Finding by Logic Regression (with Mark J. van der Laan and Chris Vulpe), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)

Multiple transcription factors coordinately control transcriptional regulation of genes in eukaryotes. Although multiple computational methods...

 

Survival Analysis

PDF

Asymptotically Optimal Model Selection Method with Right Censored Outcomes (with Mark J. van der Laan and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)

Over the last two decades, non-parametric and semi-parametric approaches that adapt well known techniques such...

 

PDF

Recurrent Events Analysis in the Presence of Time Dependent Covariates and Dependent Censoring (with Maja Miloslavsky, Mark J. van der Laan, and Steve Butler), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)

Recurrent events models have lately received a lot of attention in the literature. The majority...

 

PDF

Estimation of the Bivariate Survival Function with Generalized Bivariate Right Censored Data Structures (with Mark J. van der Laan and James M. Robins), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)

We propose a bivariate survival function estimator for a general right censored data structure that...

 

Computational Biology

PDF

Supervised detection of conserved motifs in DNA sequences with cosmo (with Oliver Bembom and Mark J. van der Laan), Statistical Applications in Genetics and Molecular Biology (2007)

A number of computational methods have been proposed for identifying transcription factor binding sites from...

 

PDF

Supervised Detection of Conserved Motifs in DNA Sequences with cosmo (with Oliver Bembom and Mark J. van der Laan), U.C. Berkeley Division of Biostatistics Working Paper Series (2006)

A number of computational methods have been proposed for identifying transcription factor binding sites from...

 

PDF

Multiple Tests of Association with Biological Annotation Metadata (with Sandrine Dudoit and Mark J. van der Laan), U.C. Berkeley Division of Biostatistics Working Paper Series (2006)

We propose a general and formal statistical framework for the multiple tests of associations between...

 

PDF

Regulatory Motif Finding by Logic Regression (with Mark J. van der Laan and Chris Vulpe), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)

Multiple transcription factors coordinately control transcriptional regulation of genes in eukaryotes. Although multiple computational methods...

 

PDF

Identification of Regulatory Elements Using A Feature Selection Method (with Mark J. van der Laan and Michael B. Eisen), U.C. Berkeley Division of Biostatistics Working Paper Series (2001)

Many methods have been described to identify regulatory motifs in the transcription control regions of...

 

Software

Link

cosmoweb: A web application for the supervised detection of conserved motifs in DNA sequences. (with Oliver Bembom and Mark Johannes van der Laan), Oliver Bembom (2006)

cosmo searches a set of unaligned DNA sequences for a shared motif that may, for...

 

Link

ccosmo: A stand-along C program for the supervised detection of conserved motifs in DNA sequences. (with Oliver Bembom and Mark Johannes van der Laan), Oliver Bembom (2006)

cosmo searches a set of unaligned DNA sequences for a shared motif that may, for...

 

Statistical Models

Supervised Detection of Regulatory Motifs in DNA Sequences (with Mark J. van der Laan, Sandrine Dudoit, Biao Xing, and Michael B. Eisen ), Statistical Applications in Genetics and Molecular Biology (2010)

Identification of transcription factor binding sites (regulatory motifs) is a major interest in contemporary biology....

 
A Non-Homogeneous Hidden-State Model on First Order Differences for Automatic Detection of Nucleosome Positions (with Pei Fen Kuan, Dana Huebert, and Audrey Gasch), Statistical Applications in Genetics and Molecular Biology (2010)

The ability to map individual nucleosomes accurately across genomes enables the study of relationships between...

 
Supervised Detection of Conserved Motifs in DNA Sequences with Cosmo (with Oliver Bembom and Mark J. van der Laan), Statistical Applications in Genetics and Molecular Biology (2010)

A number of computational methods have been proposed for identifying transcription factor binding sites from...

 

PDF

A Statistical Framework for the Analysis of ChIP-Seq Data (with Pei Fen Kuan, Dongjun Chung, Guangjin Pan, James A. Thomson, and Ron Stewart), Journal of the American Statistical Association (2009)

Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) has revolutionalized experiments for genome-wide profiling of DNA-binding proteins,...

 

PDF

Multiple Tests of Association with Biological Annotation Metadata (with Sandrine Dudoit and Mark J. van der Laan), U.C. Berkeley Division of Biostatistics Working Paper Series (2006)

We propose a general and formal statistical framework for the multiple tests of associations between...

 

PDF

Regulatory Motif Finding by Logic Regression (with Mark J. van der Laan and Chris Vulpe), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)

Multiple transcription factors coordinately control transcriptional regulation of genes in eukaryotes. Although multiple computational methods...

 

PDF

Loss-Based Estimation with Cross-Validation: Applications to Microarray Data Analysis and Motif Finding (with Sandrine Dudoit, Mark J. van der Laan, Annette M. Molinaro, Sandra E. Sinisi, and Siew Leng Teng), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)

Current statistical inference problems in genomic data analysis involve parameter estimation for high-dimensional multivariate distributions,...

 

PDF

Asymptotically Optimal Model Selection Method with Right Censored Outcomes (with Mark J. van der Laan and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)

Over the last two decades, non-parametric and semi-parametric approaches that adapt well known techniques such...

 

PDF

Recurrent Events Analysis in the Presence of Time Dependent Covariates and Dependent Censoring (with Maja Miloslavsky, Mark J. van der Laan, and Steve Butler), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)

Recurrent events models have lately received a lot of attention in the literature. The majority...

 

Statistical Theory and Methods

Asymptotic Optimality of Likelihood-Based Cross-Validation (with Mark J. van der Laan and Sandrine Dudoit), Statistical Applications in Genetics and Molecular Biology (2010)

Likelihood-based cross-validation is a statistical tool for selecting a density estimate based on n i.i.d....

 

PDF

Asymptotically Optimal Model Selection Method with Right Censored Outcomes (with Mark J. van der Laan and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)

Over the last two decades, non-parametric and semi-parametric approaches that adapt well known techniques such...

 

PDF

Asymptotic Optimality of Likelihood Based Cross-Validation (with Mark J. van der Laan and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)

Likelihood-based cross-validation is a statistical tool for selecting a density estimate based on n i.i.d....

 

PDF

Recurrent Events Analysis in the Presence of Time Dependent Covariates and Dependent Censoring (with Maja Miloslavsky, Mark J. van der Laan, and Steve Butler), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)

Recurrent events models have lately received a lot of attention in the literature. The majority...

 

PDF

Estimation of the Bivariate Survival Function with Generalized Bivariate Right Censored Data Structures (with Mark J. van der Laan and James M. Robins), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)

We propose a bivariate survival function estimator for a general right censored data structure that...

 

Computational Biology/Bioinformatics

Supervised Detection of Regulatory Motifs in DNA Sequences (with Mark J. van der Laan, Sandrine Dudoit, Biao Xing, and Michael B. Eisen ), Statistical Applications in Genetics and Molecular Biology (2010)

Identification of transcription factor binding sites (regulatory motifs) is a major interest in contemporary biology....

 
A Non-Homogeneous Hidden-State Model on First Order Differences for Automatic Detection of Nucleosome Positions (with Pei Fen Kuan, Dana Huebert, and Audrey Gasch), Statistical Applications in Genetics and Molecular Biology (2010)

The ability to map individual nucleosomes accurately across genomes enables the study of relationships between...

 
Supervised Detection of Conserved Motifs in DNA Sequences with Cosmo (with Oliver Bembom and Mark J. van der Laan), Statistical Applications in Genetics and Molecular Biology (2010)

A number of computational methods have been proposed for identifying transcription factor binding sites from...

 

PDF

A Statistical Framework for the Analysis of ChIP-Seq Data (with Pei Fen Kuan, Dongjun Chung, Guangjin Pan, James A. Thomson, and Ron Stewart), Journal of the American Statistical Association (2009)

Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) has revolutionalized experiments for genome-wide profiling of DNA-binding proteins,...

 

Link

Multiple Testing Methods For ChIP–Chip High Density Oligonucleotide Array Data (with Mark J. van der Laan, Sandrine Dudoit, and Simon E. Cawley), Journal of Computational Biology (2006)

Cawley et al. (2004) have recently mapped the locations of binding sites for three transcription...

 

PDF

Multiple Testing Methods For ChIP-Chip High Density Oligonucleotide Array Data (with Mark J. van der Laan, Sandrine Dudoit, and Simon E. Cawley), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)

Cawley et al. (2004) have recently mapped the locations of binding sites for three transcription...

 

PDF

Loss-Based Estimation with Cross-Validation: Applications to Microarray Data Analysis and Motif Finding (with Sandrine Dudoit, Mark J. van der Laan, Annette M. Molinaro, Sandra E. Sinisi, and Siew Leng Teng), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)

Current statistical inference problems in genomic data analysis involve parameter estimation for high-dimensional multivariate distributions,...