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List of works by Terrence S. Furey

A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins

scientific article

A general integrative genomic feature transcription factor binding site prediction method applied to analysis of USF1 binding in cardiovascular disease

scientific article published on April 2009

A genome-wide analysis of open chromatin in human epididymis epithelial cells reveals candidate regulatory elements for genes coordinating epididymal function

scientific article

A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function

scientific article (publication date: May 2012)

A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data.

scientific article

A physical map of the human genome

scientific article

A predictive framework for integrating disparate genomic data types using sample-specific gene set enrichment analysis and multi-task learning

scientific article

Abstract B44: Chromatin structure impacts androgen receptor transcriptional specificity in prostate cancer cell lines

Allele-specific and heritable chromatin signatures in humans

scientific article published on 16 September 2010

Alterations to chromatin in intestinal macrophages link IL-10 deficiency to inappropriate inflammatory responses

scientific article published on 9 May 2016

Analysis of complex disease association and linkage studies using the University of California Santa Cruz Genome Browser

scientific article

Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain

scientific article

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells

scientific article

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions ⬇️

scientific article published on October 23, 2012

Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma

scientific article

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity

scientific article

Colonic Epithelial miR-31 Associates with the Development of Crohn's Phenotypes

Comparative recombination rates in the rat, mouse, and human genomes

scientific article published on April 2004

Comparison of human (and other) genome browsers

scientific article

Correcting nucleotide-specific biases in high-throughput sequencing data

scientific article

Correction: A Predictive Framework for Integrating Disparate Genomic Data Types Using Sample-Specific Gene Set Enrichment Analysis and Multi-Task Learning

scientific article published in PLoS ONE

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution

scientific article

DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types

scientific article published on 8 May 2013

DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2

scientific article

DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter

scientific article

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

scientific article

Evidence of Influence of Genomic DNA Sequence on Human X Chromosome Inactivation

article

Evidence of influence of genomic DNA sequence on human X chromosome inactivation

scientific article published on 17 July 2006

Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection

scientific article

F-Seq: a feature density estimator for high-throughput sequence tags

scientific article

GSAASeqSP: a toolset for gene set association analysis of RNA-Seq data

scientific article

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

scientific article

Genetic and epigenetic determinants of inter-individual variability in responses to toxicants

article

Genetics. Genetics driving epigenetics

scientific article

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

scientific article

Genome-wide sequence and functional analysis of early replicating DNA in normal human fibroblasts

scientific article

Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells.

scientific article published on 29 August 2017

Genomic sweeping for hypermethylated genes

scientific article published on 5 December 2006

Global Epigenomic Analysis of Primary Human Pancreatic Islets Provides Insights into Type 2 Diabetes Susceptibility Loci

Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci

scientific article

Heritable individual-specific and allele-specific chromatin signatures in humans

scientific article

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

scientific article

High-resolution mapping and characterization of open chromatin across the genome

scientific article

High-resolution mapping studies of chromatin and gene regulatory elements

scientific article

Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome

scientific article

Identifying and characterizing regulatory sequences in the human genome with chromatin accessibility assays

scientific article published on 15 October 2012

Increased Colonic Expression of ACE2 Associates with Poor Prognosis in Crohn's disease

scientific article published on 24 November 2020

Initial sequencing and analysis of the human genome

scientific article published on 15 February 2001

Initial sequencing and comparative analysis of the mouse genome

scientific article

Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets

scientific article published on 22 September 2011

Integration of cytogenetic landmarks into the draft sequence of the human genome

scientific article published in Nature

Integration of the cytogenetic map with the draft human genome sequence

scientific article

Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation

scientific article published on 21 January 2020

Knowledge-based analysis of microarray gene expression data by using support vector machines

scientific article

MicroRNAs Classify Different Disease Behavior Phenotypes of Crohn's Disease and May Have Prognostic Utility

scientific article

Molecular classification of Crohn's disease reveals two clinically relevant subtypes.

scientific article published on 14 October 2016

Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes

scientific article

New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk ⬇️

scientific article published on February 2016

Novel distal eQTL analysis demonstrates effect of population genetic architecture on detecting and interpreting associations

scientific article

O-004 Analysis of Chromatin and Transcriptional Profiles in Crohnʼs Disease Reveals Molecular Subclasses and Highlights Functional Regulatory Regions Implicated in Disease

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

scientific article

P-193 A Distinct Microbiome Signature Characterizes Patients with Penetrating and Fistulizing Crohnʼs Disease

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

scientific article published on 12 March 2013

Redefining the IBDs using genome-scale molecular phenotyping

scientific article published on 01 May 2019

Removing reference mapping biases using limited or no genotype data identifies allelic differences in protein binding at disease-associated loci

scientific article

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

scientific article

Support vector machine classification and validation of cancer tissue samples using microarray expression data

scientific article

The DNA sequence and biology of human chromosome 19

scientific article

The DNA sequence of human chromosome 7

scientific article

The UCSC Genome Browser Database: update 2006

scientific article

The accessible chromatin landscape of the human genome

scientific article

The human genome browser at UCSC

scientific article

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)

scientific article

The structure and evolution of centromeric transition regions within the human genome

scientific article published on 01 August 2004

Tissue- and strain-specific effects of a genotoxic carcinogen 1,3-butadiene on chromatin and transcription

scientific article published on 10 February 2018

Tu1927 Genetically Driven Chromatin Organization Identifies Regulatory SNPs Associated With Crohn's Disease

Variation in DNA-Damage Responses to an Inhalational Carcinogen (1,3-Butadiene) in Relation to Strain-Specific Differences in Chromatin Accessibility and Gene Transcription Profiles in C57BL/6J and CAST/EiJ Mice

scientific article

Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects

scientific article published on 24 October 2013

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