Katherine S. Pollard

发表

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes

Ian Korf, Danielle G. Lemay, Angie S. Hinrichs, 2012, BMC Bioinformatics.

lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements

Nir Yosef, Jingjing Zhao, Anat Kreimer, 2020, Nature Protocols.

New Methods for Detecting Lineage-Specific Selection

David Haussler, Adam C. Siepel, Katherine S. Pollard, 2006, RECOMB.

PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data

Jonathan A. Eisen, Katherine S. Pollard, Steven W. Kembel, 2011, PLoS Comput. Biol..

ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin

Katherine S. Pollard, John A. Capra, Alexander G. Williams, 2012, PLoS Comput. Biol..

The UCSC Archaeal Genome Browser

Katherine S. Pollard, Todd M. Lowe, Andy Pohl, 2005, Nucleic Acids Res..

Cluster Analysis of Genomic Data with Applications in R

Mark J. van der Laan, Katherine S. Pollard, K. Pollard, 2005 .

Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource

Jonathan A. Eisen, Katherine S. Pollard, Dongying Wu, 2012, BMC Bioinformatics.

High-throughput sequencing of the DBA/2J mouse genome

Lu Lu, Deanna M. Church, Richa Agarwala, 2010, BMC Bioinformatics.

Multiple Testing for Gene Expression Data: An Investigation of Null Distributions with Consequences for the Permutation Test

Mark J. van der Laan, Katherine S. Pollard, K. Pollard, 2003, METMBS.

Features of ChIP-seq data peak calling algorithms with good operating characteristics Running Title : Benchmark ChIP-seq peak calling algorithms

Katherine S. Pollard, Sean Thomas, Reuben Thomas, 2016 .

Semi-supervised identification of cell populations in single-cell ATAC-seq

Katherine S. Pollard, Pawel F. Przytycki, K. Pollard, 2019, bioRxiv.

A Method to Identify Signicant Clusters in Gene Expression Data

Mark J. van der Laan, Katherine S. Pollard, 2002 .

Cluster Analysis of Genomic Data

Katherine S. Pollard, M. J. van der Laan, 2005 .

Cell Layers: Uncovering clustering structure and knowledge in unsupervised single-cell transcriptomic analysis

Katherine S. Pollard, Pawel F. Przytycki, Benoit G. Bruneau, 2020, bioRxiv.

MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome

Katherine S. Pollard, Michael A. Fischbach, Stephen Nayfach, 2015, Bioinform..

CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues

Katherine S. Pollard, Pawel F. Przytycki, K. Pollard, 2019, Genome biology.

PHAST and RPHAST: phylogenetic analysis with space/time models

Adam C. Siepel, Katherine S. Pollard, Melissa J. Hubisz, 2011, Briefings Bioinform..

Unboxing cluster heatmaps

Alark Joshi, Sophie Engle, Sean Whalen, 2017, BMC Bioinformatics.

New insights from uncultivated genomes of the global human gut microbiome

Katherine S. Pollard, Nikos C. Kyrpides, Stephen Nayfach, 2019, Nature.

Gene regulatory networks in lactation: identification of global principles using bioinformatics

Danielle G. Lemay, J. Bruce German, Katherine S. Pollard, 2007, BMC Systems Biology.

Integrating Diverse Datasets Improves Developmental Enhancer Prediction

Katherine S. Pollard, Nadav Ahituv, Dennis Kostka, 2013, PLoS Comput. Biol..

Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species

Katherine S. Pollard, Aram Avila-Herrera, 2015 .

A Method to Identify Significant Clusters in Gene Expression Data

Mark J. van der Laan, Katherine S. Pollard, K. Pollard, 2002 .

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes

Jonathan A. Eisen, Katherine S. Pollard, Thomas J. Sharpton, 2015, bioRxiv.

Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species

Katherine S. Pollard, Aram Avila-Herrera, K. Pollard, 2015, BMC Bioinformatics.

Features that define the best ChIP-seq peak calling algorithms

Katherine S. Pollard, Reuben Thomas, Sean Thomas, 2016, Briefings Bioinform..

Resampling-Based Multiple Hypothesis Testing with Applications to Genomics: New Developments in the R/Bioconductor Package multtest

Sandrine Dudoit, Katherine S. Pollard, Mark J. van der Laan, 2009 .

Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults

Katherine S. Pollard, Thomas Deiss, Joseph L. DeRisi, 2018, Proceedings of the National Academy of Sciences.

Statistical inference for simultaneous clustering of gene expression data.

Mark J. van der Laan, Katherine S. Pollard, M. J. van der Laan, 2002, Mathematical biosciences.

Resampling-based multiple testing with asymptotic strong control of type I error

Mark J. van der Laan, Katherine S. Pollard, K. Pollard, 2003 .

Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States

Rob Knight, Jack A. Gilbert, Katherine S. Pollard, 2013, Science.

American Gut: an Open Platform for Citizen-Science Microbiome Research

Rob Knight, Pieter C. Dorrestein, Hosein Mohimani, 2018 .

Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates

Sandrine Dudoit, Katherine S. Pollard, Mark J. van der Laan, 2004, Statistical applications in genetics and molecular biology.

Chromosomal haplotypes by genetic phasing of human families.

Jared C. Roach, Gustavo Glusman, David J. Galas, 2011, American journal of human genetics.

SIRT1 and SIRT3 Deacetylate Homologous Substrates: AceCS1,2 and HMGCS1,2

Eric Verdin, Katherine S. Pollard, K. Pollard, 2011, Aging.

Hybrid Clustering of Gene Expression Data with Visualization and the Bootstrap

Mark J. van der Laan, Katherine S. Pollard, K. Pollard, 2001 .

Analysis of Human Accelerated DNA Regions Using Archaic Hominin Genomes

Janet Kelso, Richard E. Green, Katherine S. Pollard, 2012, PloS one.

Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate

Sandrine Dudoit, Katherine S. Pollard, Mark J. van der Laan, 2004, Statistical applications in genetics and molecular biology.

Chromatin features constrain structural variation across evolutionary timescales

Katherine S. Pollard, K. Pollard, G. Fudenberg, 2018, Proceedings of the National Academy of Sciences.

Signatures of accelerated somatic evolution in gene promoters in multiple cancer types

Brent S. Pedersen, Subhajyoti De, Katherine S. Pollard, 2015, Nucleic acids research.

Multiple Testing Procedures: the multtest Package and Applications to Genomics

Sandrine Dudoit, Katherine S. Pollard, S. Dudoit, 2005 .

A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome

Robert D. Finn, Katherine S. Pollard, Nicola Segata, 2019, bioRxiv.

A new algorithm for hybrid hierarchical clustering with visualization and the bootstrap

Mark J. van der Laan, Katherine S. Pollard, K. Pollard, 2003 .

A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes

Katherine S. Pollard, Dennis Kostka, Melissa J. Hubisz, 2013, PLoS genetics.

Noncoding Sequences Near Duplicated Genes Evolve Rapidly

Katherine S. Pollard, Dennis Kostka, Matthew W. Hahn, 2010, Genome biology and evolution.

A unified catalog of 204,938 reference genomes from the human gut microbiome

Robert D. Finn, Katherine S. Pollard, Nicola Segata, 2020, Nature Biotechnology.

The Phylogenetic Diversity of Metagenomes

Jonathan A. Eisen, Katherine S. Pollard, Steven W. Kembel, 2011, PloS one.

The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome

Katherine S. Pollard, Dennis Kostka, Melissa J. Hubisz, 2011, Molecular biology and evolution.

New methods for identifying significant clusters in gene expression data

Katherine S. Pollard, K. Pollard, 2022 .

American Gut: an Open Platform for Citizen Science Microbiome Research

Rob Knight, Pieter C. Dorrestein, Hosein Mohimani, 2018, mSystems.

Many human accelerated regions are developmental enhancers

Katherine S. Pollard, Genevieve D. Erwin, K. Pollard, 2013, Philosophical Transactions of the Royal Society B: Biological Sciences.

Paired and Unpaired Comparisons and Clustering with Gene Expression Data

Mark J. van der Laan, Katherine S. Pollard, Jennifer Bryan, 2001 .

Test Statistics Null Distributions in Multiple Testing: Simulation Studies and Applications to Genomics

Sandrine Dudoit, Katherine S. Pollard, Mark J. van der Laan, 2005 .

Multiple Testing Procedures and Applications to Genomics

Sandrine Dudoit, Katherine S. Pollard, S. Dudoit, 2004 .

AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design

Bruce R. Conklin, Sean Whalen, Katherine S. Pollard, 2019, Genome Biology.

Chromatin remodelling complex dosage modulates transcription factor function in heart development

R. Mark Henkelman, Ru-Fang Yeh, Katherine S. Pollard, 2011, Nature communications.

Choice of a null distribution in resampling-based multiple testing

Mark J. van der Laan, Katherine S. Pollard, K. Pollard, 2004 .

Ongoing GC-Biased Evolution Is Widespread in the Human Genome and Enriched Near Recombination Hot Spots

David Haussler, Katherine S. Pollard, Sol Katzman, 2011, Genome biology and evolution.