List of works - Jeffrey T. Leek

A computationally efficient modular optimal discovery procedure

scientific article published on 24 December 2010

A decision-theory approach to interpretable set analysis for high-dimensional data

scientific article

A general framework for multiple testing dependence

scholarly article

A randomized trial in a massive online open course shows people don't know what a statistically significant relationship looks like, but they can learn.

scientific article

A simple and reproducible breast cancer prognostic test.

scientific article

A statistical approach to selecting and confirming validation targets in -omics experiments

scientific article

A visual tool for defining reproducibility and replicability

scientific article published on 01 July 2019

Addressing confounding artifacts in reconstruction of gene co-expression networks

article

Addressing confounding artifacts in reconstruction of gene co-expression networks

An estimate of the science-wise false discovery rate and application to the top medical literature

scientific article published on 25 September 2013

Asymptotic conditional singular value decomposition for high-dimensional genomic data.

scientific article

Ballgown bridges the gap between transcriptome assembly and expression analysis

scientific article published on March 2015

BatchQC: interactive software for evaluating sample and batch effects in genomic data

scientific article

Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies.

scientific article published in February 2012

Capturing heterogeneity in gene expression studies by surrogate variable analysis

scientific article

Cloud-scale RNA-sequencing differential expression analysis with Myrna

scientific article

Cooperation between referees and authors increases peer review accuracy

scientific article

Corrigendum: Differential expression analysis of RNA-seq data at single-base resolution.

scientific article published in July 2014

Developmental regulation of human cortex transcription and its clinical relevance at single base resolution

scientific article

Differential expression analysis of RNA-seq data at single-base resolution

scientific article

Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study

scientific article

EDGE: extraction and analysis of differential gene expression

scientific article published on 15 December 2005

Erratum to: Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis

scientific article published on 10 August 2016

Evolution of cellular morpho-phenotypes in cancer metastasis.

scientific article

Flexible expressed region analysis for RNA-seq with derfinder

scientific article published on 29 September 2016

Flexible expressed region analysis for RNA-seq with derfinder

scholarly article published 19 February 2015

Gene expression anti-profiles as a basis for accurate universal cancer signatures

scientific article

Gene set bagging for estimating the probability a statistically significant result will replicate

scientific article

Human splicing diversity across the Sequence Read Archive

scientific article published on 29 January 2016

Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive

scientific article

Improving the value of public RNA-seq expression data by phenotype prediction.

scientific article published in May 2018

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

scientific article published on 13 January 2022

Measurement, Summary, and Methodological Variation in RNA-sequencing

scientific article published in 2014

On the design and analysis of gene expression studies in human populations

article

Opinion: Reproducible research can still be wrong: adopting a prevention approach

scientific article

Personalized medicine: Keep a way open for tailored treatments

scientific article (publication date: 18 April 2012)

Polyester: simulating RNA-seq datasets with differential transcript expression

scientific article published on 28 April 2015

Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis

scientific article

Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction

scientific article published on 6 June 2014

Publisher Correction: A visual tool for defining reproducibility and replicability

scientific article published on 01 August 2019

Rail-RNA: Scalable analysis of RNA-seq splicing and coverage

scientific article published on 7 May 2015

Rail-RNA: scalable analysis of RNA-seq splicing and coverage

scientific article

Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce

scientific article

Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce

scientific article published on 24 December 2015

ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets

scientific article

Recounting the FANTOM CAGEAssociated Transcriptome

scientific article published on 20 February 2020

Removing batch effects for prediction problems with frozen surrogate variable analysis.

scientific article published on 23 September 2014

Sequencing technology does not eliminate biological variability

scientific article published on 11 July 2011

Sequestration: inadvertently killing biomedical research to score political points

scientific article published on 27 March 2013

Significance analysis and statistical dissection of variably methylated regions

scientific article published on 17 June 2011

Significance analysis of time course microarray experiments

scientific article

Statistics. What is the question?

scientific article

Statistics: P values are just the tip of the iceberg.

scientific article published on April 2015

Surrogate Variable Analysis ⬇️

doctoral thesis by Jeffrey Tullis Leek, University of Washington, 2007

Systems-level dynamic analyses of fate change in murine embryonic stem cells

scientific article

Tackling the widespread and critical impact of batch effects in high-throughput data

scientific article (publication date: October 2010)

Temporal dynamics and genetic control of transcription in the human prefrontal cortex

scientific article

Test set bias affects reproducibility of gene signatures

scientific article published on 18 March 2015

The Joint Null Criterion for Multiple Hypothesis Tests

The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments

scientific article published on 23 August 2006

The practical effect of batch on genomic prediction

scientific article published on January 2012

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

scientific article published on 17 January 2012

qSVA framework for RNA quality correction in differential expression analysis

scientific article

recount-brain: a curated repository of human brain RNA-seq datasets metadata

scholarly article published 24 April 2019

regionReport: Interactive reports for region-level and feature-level genomic analyses

scientific article published on May 2015

List of works by Jeffrey T. Leek

A computationally efficient modular optimal discovery procedure

A decision-theory approach to interpretable set analysis for high-dimensional data

A general framework for multiple testing dependence

A randomized trial in a massive online open course shows people don't know what a statistically significant relationship looks like, but they can learn.

A simple and reproducible breast cancer prognostic test.

A statistical approach to selecting and confirming validation targets in -omics experiments

A visual tool for defining reproducibility and replicability

Addressing confounding artifacts in reconstruction of gene co-expression networks

Addressing confounding artifacts in reconstruction of gene co-expression networks

An estimate of the science-wise false discovery rate and application to the top medical literature

Asymptotic conditional singular value decomposition for high-dimensional genomic data.

Ballgown bridges the gap between transcriptome assembly and expression analysis

BatchQC: interactive software for evaluating sample and batch effects in genomic data

Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies.

Capturing heterogeneity in gene expression studies by surrogate variable analysis

Cloud-scale RNA-sequencing differential expression analysis with Myrna

Cooperation between referees and authors increases peer review accuracy

Corrigendum: Differential expression analysis of RNA-seq data at single-base resolution.

Developmental regulation of human cortex transcription and its clinical relevance at single base resolution

Differential expression analysis of RNA-seq data at single-base resolution

Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study

EDGE: extraction and analysis of differential gene expression

Erratum to: Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis

Evolution of cellular morpho-phenotypes in cancer metastasis.

Flexible expressed region analysis for RNA-seq with derfinder

Flexible expressed region analysis for RNA-seq with derfinder

Gene expression anti-profiles as a basis for accurate universal cancer signatures

Gene set bagging for estimating the probability a statistically significant result will replicate

Human splicing diversity across the Sequence Read Archive

Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive

Improving the value of public RNA-seq expression data by phenotype prediction.

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

Measurement, Summary, and Methodological Variation in RNA-sequencing

On the design and analysis of gene expression studies in human populations

Opinion: Reproducible research can still be wrong: adopting a prevention approach

Personalized medicine: Keep a way open for tailored treatments

Polyester: simulating RNA-seq datasets with differential transcript expression

Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis

Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction

Publisher Correction: A visual tool for defining reproducibility and replicability

Rail-RNA: Scalable analysis of RNA-seq splicing and coverage

Rail-RNA: scalable analysis of RNA-seq splicing and coverage

Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce

Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce

ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets

Recounting the FANTOM CAGEAssociated Transcriptome

Removing batch effects for prediction problems with frozen surrogate variable analysis.

Sequencing technology does not eliminate biological variability

Sequestration: inadvertently killing biomedical research to score political points

Significance analysis and statistical dissection of variably methylated regions

Significance analysis of time course microarray experiments

Statistics. What is the question?

Statistics: P values are just the tip of the iceberg.

Surrogate Variable Analysis ⬇️

Systems-level dynamic analyses of fate change in murine embryonic stem cells

Tackling the widespread and critical impact of batch effects in high-throughput data

Temporal dynamics and genetic control of transcription in the human prefrontal cortex

Test set bias affects reproducibility of gene signatures

The Joint Null Criterion for Multiple Hypothesis Tests

The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments

The practical effect of batch on genomic prediction

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

qSVA framework for RNA quality correction in differential expression analysis

recount-brain: a curated repository of human brain RNA-seq datasets metadata

regionReport: Interactive reports for region-level and feature-level genomic analyses