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Summarizing and correcting the GC content bias in high-throughput sequencing

Nucleic acids research, 2012-05, Vol.40 (10), p.e72

2012

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Normalization of RNA-seq data using factor analysis of control genes or samples

Nature biotechnology, 2014-09, Vol.32 (9), p.896-902

2014

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GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly

Genome research, 2017-12, Vol.27 (12), p.2050

2017

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RLE plots: Visualizing unwanted variation in high dimensional data

PloS one, 2018-02, Vol.13 (2), p.e0191629-e0191629

2018

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A quartet of PIF bHLH factors provides a transcriptionally centered signaling hub that regulates seedling morphogenesis through differential expression-patterning of shared target genes in Arabidopsis

PLoS genetics, 2013-01, Vol.9 (1), p.e1003244-e1003244

2013

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A Tetrahymena Piwi Bound to Mature tRNA 3′ Fragments Activates the Exonuclease Xrn2 for RNA Processing in the Nucleus

Molecular cell, 2012-11, Vol.48 (4), p.509-520

2012

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The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program "CASCADE"

PLoS medicine, 2016-12, Vol.13 (12), p.e1002204-e1002204

2016

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Network inference using informative priors

Proceedings of the National Academy of Sciences - PNAS, 2008-09, Vol.105 (38), p.14313-14318

2008

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A statistical framework for analyzing deep mutational scanning data

Genome Biology, 2017-08, Vol.18 (1), p.150-150, Article 150

2017

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The healthy ageing gene expression signature for Alzheimer's disease diagnosis: a random sampling perspective

Genome Biology, 2018-07, Vol.19 (1), p.97-97, Article 97

2018

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GOstat: find statistically overrepresented Gene Ontologies within a group of genes

Bioinformatics, 2004-06, Vol.20 (9), p.1464-1465

2004

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Genome-wide analysis of glucocorticoid receptor binding regions in adipocytes reveal gene network involved in triglyceride homeostasis

PloS one, 2010-12, Vol.5 (12), p.e15188

2010

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

Molecular systems biology, 2020-06, Vol.16 (6), p.e9389-n/a

2020

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

Proceedings of the National Academy of Sciences - PNAS, 2019-05, Vol.116 (20), p.9775-9784

2019

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Identification of cancer sex-disparity in the functional integrity of p53 and its X chromosome network

Nature communications, 2019-11, Vol.10 (1), p.5385-12, Article 5385

2019

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A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development

Cell, 2021-10, Vol.184 (22), p.5541-5558.e22

2021

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Comparing somatic mutation-callers: beyond Venn diagrams

BMC bioinformatics, 2013-06, Vol.14 (1), p.189-189, Article 189

2013

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Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments

Nature communications, 2023-05, Vol.14 (1), p.2697-2697, Article 2697

2023

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A genotype calling algorithm for affymetrix SNP arrays

Bioinformatics, 2006-01, Vol.22 (1), p.7-12

2006

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A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6

Bioinformatics, 2009-09, Vol.25 (17), p.2149-2156

2009

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Normalizing and Integrating Metabolomics Data

Analytical chemistry (Washington), 2012-12, Vol.84 (24), p.10768-10776

2012

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Changes in ferrous iron and glutathione promote ferroptosis and frailty in aging Caenorhabditis elegans

eLife, 2020-07, Vol.9

2020

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Finding a suitable library size to call variants in RNA-Seq

BMC bioinformatics, 2020-12, Vol.21 (1), p.553-553, Article 553

2020

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Strategies to enable large-scale proteomics for reproducible research

Nature communications, 2020-07, Vol.11 (1), p.3793-3793, Article 3793

2020

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Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data

Journal of the American Statistical Association, 2002-03, Vol.97 (457), p.77-87

2002

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Summarizing and correcting the GC content bias in high-throughput sequencing

Normalization of RNA-seq data using factor analysis of control genes or samples

GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly

RLE plots: Visualizing unwanted variation in high dimensional data

A quartet of PIF bHLH factors provides a transcriptionally centered signaling hub that regulates seedling morphogenesis through differential expression-patterning of shared target genes in Arabidopsis

A Tetrahymena Piwi Bound to Mature tRNA 3′ Fragments Activates the Exonuclease Xrn2 for RNA Processing in the Nucleus

The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program "CASCADE"

Network inference using informative priors

A statistical framework for analyzing deep mutational scanning data

The healthy ageing gene expression signature for Alzheimer's disease diagnosis: a random sampling perspective

GOstat: find statistically overrepresented Gene Ontologies within a group of genes

Genome-wide analysis of glucocorticoid receptor binding regions in adipocytes reveal gene network involved in triglyceride homeostasis

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

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

Identification of cancer sex-disparity in the functional integrity of p53 and its X chromosome network

A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development

Comparing somatic mutation-callers: beyond Venn diagrams

Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments

A genotype calling algorithm for affymetrix SNP arrays

A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6

Normalizing and Integrating Metabolomics Data

Changes in ferrous iron and glutathione promote ferroptosis and frailty in aging Caenorhabditis elegans

Finding a suitable library size to call variants in RNA-Seq

Strategies to enable large-scale proteomics for reproducible research

Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data

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