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List of works by Katherine Pollard

A Chromatin Accessibility Atlas of the Developing Human Telencephalon

scientific article published on 24 June 2020

A De Novo Shape Motif Discovery Algorithm Reveals Preferences of Transcription Factors for DNA Shape Beyond Sequence Motifs

scientific article published on 16 January 2019

A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome

article

A communal catalogue reveals Earth's multiscale microbial diversity

scientific article published in November 2017

A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design.

scientific article

A genome-wide approach to identifying novel-imprinted genes.

scientific article

A high-resolution map of human evolutionary constraint using 29 mammals

scientific article

A high-resolution, chromosome-assigned Komodo dragon genome reveals adaptations in the cardiovascular, muscular, and chemosensory systems of monitor lizards

scientific article published on 15 February 2019

A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes

scientific article

A most wanted list of conserved microbial protein families with no known domains

scientific article published in PLoS ONE

A nearly exhaustive search for CpG islands on whole chromosomes

scientific article published on 7 May 2009

A new partitioning around medoids algorithm

A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter

scientific article published on 8 January 2014

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

scientific article published on 20 July 2020

Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor

scientific article published on 29 December 2015

Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster

scientific article published on 26 June 2008

Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells

scientific article

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

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

scientific article published on 15 August 2019

American Gut: an Open Platform for Citizen Science Microbiome Research

article

Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy

scientific article published on 04 December 2020

An RNA gene expressed during cortical development evolved rapidly in humans

scientific article

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

scientific article published on 18 October 2016

Analysis of human accelerated DNA regions using archaic hominin genomes

scientific article

Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives.

scientific article published on 15 June 2004

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

scientific article published on 30 October 2020

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes

scientific article published on 13 November 2015

Automated and accurate estimation of gene family abundance from shotgun metagenomes

article

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

scientific article

Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus

scientific article

Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis

scientific article

Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion

scientific article

Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates

scientific article published on 18 April 2020

Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates

scientific article published on 21 August 2020

Building a chemical blueprint for human blood

scientific article published on 11 November 2020

Can a few non-coding mutations make a human brain?

scientific article

Chromatin features constrain structural variation across evolutionary timescales

article published in the Proceedings of the National Academy of Sciences of the United States of America

Chromatin remodelling complex dosage modulates transcription factor function in heart development

scientific article

Chromosomal haplotypes by genetic phasing of human families

scientific article

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

scientific article published on 25 August 2015

Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis

scientific article published on 01 December 2018

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms

scientific article published on 15 October 2020

Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis

scientific article

Composite interval mapping to identify quantitative trait loci for point-mass mixture phenotypes.

scientific article published in February 2010

Consent insufficient for data release-Response

scientific article published on 01 May 2019

Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming

scientific article published on 01 July 2019

Continental-scale distributions of dust-associated bacteria and fungi.

scientific article

Cooking shapes the structure and function of the gut microbiome

scientific article published on 30 September 2019

Cooperative activation of cardiac transcription through myocardin bridging of paired MEF2 sites

scientific article

Detection of nonneutral substitution rates on mammalian phylogenies

scientific article published on 26 October 2009

Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice

scientific article published on 5 September 2017

Developmental Loci Harbor Clusters of Accelerated Regions That Evolved Independently in Ape Lineages

scientific article published on 01 August 2018

Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases

scientific article

Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development

scientific article

Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage

scientific article published on 12 September 2012

Early-Career Scientists Shaping the World

scientific article published on 07 May 2019

Empirical Bayes accomodation of batch-effects in microarray data using identical replicate reference samples: application to RNA expression profiling of blood from Duchenne muscular dystrophy patients

scientific article

Empowering statistical methods for cellular and molecular biologists

scientific article published on 01 June 2019

Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin

scientific article published on 04 April 2016

Erratum: Global marine bacterial diversity peaks at high latitudes in winter

article

Evaluation of two methods to estimate and monitor bird populations

scientific article

Evolution of Mechanisms that Control Mating in Drosophila Males

scientific article published on 01 May 2019

Evolution of lysine acetylation in the RNA polymerase II C-terminal domain

scientific article

Evolutionary constraint and innovation across hundreds of placental mammals

scientific article published on 28 April 2023

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

scientific article published on 23 January 2019

Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes

scientific article published on 01 September 2018

Exome capture from saliva produces high quality genomic and metagenomic data

scientific article

Exploring the genesis and functions of Human Accelerated Regions sheds light on their role in human evolution

scientific article

Features that define the best ChIP-seq peak calling algorithms

scientific article

Forces Shaping the Fastest Evolving Regions in the Human Genome

Forces shaping the fastest evolving regions in the human genome

scientific article

From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome

scientific article

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

scientific article

GC-biased evolution near human accelerated regions

scientific article

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

scientific article

Genes Expressed in Specific Areas of the Human Fetal Cerebral Cortex Display Distinct Patterns of Evolution ⬇️

scientific article published on March 18, 2011

Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards

scientific article published on 29 July 2019

Genomic analyses for age at menarche identify 389 independent signals and indicate BMI-independent effects of puberty timing on cancer susceptibility

scientific article published on 23 September 2016

Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk

scientific article published on 24 April 2017

Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions

scientific article published on 12 February 2015

Genomic approaches to studying human-specific developmental traits

scientific article

Gibbon genome and the fast karyotype evolution of small apes

scientific article

Global ecotypes in the ubiquitous marine clade SAR86

scientific article published on 14 October 2019

Global marine bacterial diversity peaks at high latitudes in winter

scientific article

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

scientific article published on 23 July 2010

Hotspots of biased nucleotide substitutions in human genes

scientific article

How do they measure up? Differences in stakeholder perceptions of quality measures used in English community nursing

scientific article published on 08 October 2019

How old is my gene? ⬇️

scientific article (publication date: November 2013)

Human disease modeling reveals integrated transcriptional and epigenetic mechanisms of NOTCH1 haploinsufficiency

scientific article

Human evolution: the non-coding revolution

scientific article published on 2 October 2017

Hypothesis tests for point-mass mixture data with application to 'omics data with many zero values

scientific article

Identifying genetic networks underlying myometrial transition to labor

scientific article

Integrating diverse datasets improves developmental enhancer prediction

scientific article

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

article published in the Proceedings of the National Academy of Sciences of the United States of America

Joint mouse-human phenome-wide association to test gene function and disease risk

scientific article

Many human accelerated regions are developmental enhancers

scientific article (publication date: 19 December 2013)

Marked seasonal variation in the wild mouse gut microbiota

scientific article published on 29 May 2015

Massively parallel dissection of human accelerated regions in human and chimpanzee neural progenitors

Measuring quality in community nursing: a mixed-methods study

Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth

scientific article published on 08 April 2020

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

scientific article published on 22 June 2015

Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota.

scientific article published on 24 November 2016

Molecular basis of CTCF binding polarity in genome folding

scientific article published on 05 November 2020

Most chromatin interactions are not in linkage disequilibrium

Multiple testing. Part I. Single-step procedures for control of general type I error rates

scientific article published on 9 June 2004

Multiple testing. Part II. Step-down procedures for control of the family-wise error rate

scientific article published on 14 June 2004

New Methods for Detecting Lineage-Specific Selection

New insights from uncultivated genomes of the global human gut microbiome

scientific article published on 13 March 2019

Noncoding sequences near duplicated genes evolve rapidly

scientific article

Novel bacterial taxa in the human microbiome

scientific article

Novel genes exhibit distinct patterns of function acquisition and network integration ⬇️

scientific article published on December 27, 2010

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

scientific article published on June 21, 2011

PHAST and RPHAST: phylogenetic analysis with space/time models

scientific article

PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.

scientific article

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization

article

Population Genetics in the Human Microbiome

scientific article published on 25 November 2019

Predicting 3D genome folding from DNA sequence with Akita

scientific article published on 12 October 2020

Principles of meiotic chromosome assembly revealed in S. cerevisiae

scientific article published on 22 October 2019

Profile hidden Markov models for the detection of viruses within metagenomic sequence data

scientific article

ProteinHistorian: tools for the comparative analysis of eukaryote protein origin

scientific article

Proteobacteria explain significant functional variability in the human gut microbiome.

scientific article published on 23 March 2017

Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States

scientific article

Reply to 'Inflated performance measures in enhancer-promoter interaction-prediction methods'

scientific article published on 01 August 2019

SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells

scientific article published on 7 March 2016

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

scientific article

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

scientific article published on May 2015

Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community

scientific article published on 13 April 2022

Single-cell epigenomics reveals mechanisms of human cortical development

scientific article published on 06 October 2021

Statistical inference for simultaneous clustering of gene expression data

scientific article

Substitution patterns are GC-biased in divergent sequences across the metazoans

scientific article

Supervised distance matrices

scientific article

The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation

scientific article published on 15 November 2017

The UCSC Archaeal Genome Browser

scientific article

The bovine lactation genome: insights into the evolution of mammalian milk

scientific article

The importance of being cis: evolution of orthologous fish and mammalian enhancer activity.

scientific article

The phylogenetic diversity of metagenomes

scientific article

The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome

scientific article

Three-dimensional genome rewiring in loci with human accelerated regions ⬇️

scientific article published on 28 April 2023

Topical Silver Diamine Fluoride for Dental Caries Arrest in Preschool Children: A Randomized Controlled Trial and Microbiological Analysis of Caries Associated Microbes and Resistance Gene Expression

scientific article published on 30 August 2017

Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges

scientific article

Toward unrestricted use of public genomic data:

scientific article

Transcription factor protein interactomes reveal genetic determinants in heart disease

scientific article published in March 2022

Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach

scientific article

Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum.

scientific article

Transcriptomic and epigenomic characterization of the developing bat wing

scientific article published on 28 March 2016

Unboxing cluster heatmaps

scientific article

Urban greenness influences airborne bacterial community composition

scientific article published on 11 July 2016

What Makes Us Human?

scientific article published on 01 May 2009

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

scientific article published on 08 July 2020

motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences

scientific article

phylogenize: correcting for phylogeny reveals genes associated with microbial distributions

scientific article published on 01 February 2020

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