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List of works by Nathan C. Sheffield

A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles

scientific article published on 08 September 2008

Analytical Approaches for ATAC-seq Data Analysis

scientific article published on 01 June 2020

Augmented Interval List: a novel data structure for efficient genomic interval search

scientific article published on 01 December 2019

BART: a transcription factor prediction tool with query gene sets or epigenomic profiles

scientific article published on 28 March 2018

BART: a transcription factor prediction tool with query gene sets or epigenomic profiles

article

Bedshift: perturbation of genomic interval sets

scientific article

COCOA: coordinate covariation analysis of epigenetic heterogeneity

scientific article published on 07 September 2020

Calculating expected DNA remnants from ancient founding events in human population genetics

scientific article

ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors.

scientific article published on 17 August 2015

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity

scientific article

Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines

scientific article

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features.

scientific article published in July 2018

DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma.

scientific article

Data Integration with SUMO Detects Latent Relationships Between Patients in Lower-Grade Gliomas

scientific article

Differential DNA Methylation Analysis without a Reference Genome

scientific article

Epigenome mapping reveals distinct modes of gene regulation and widespread enhancer reprogramming by the oncogenic fusion protein EWS-FLI1.

scientific article

Expanding the Galaxy’s reference data

scientific article

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

scientific article

From biomedical cloud platforms to microservices: next steps in FAIR data and analysis

scientific article published on 8 September 2022

GA4GH: International policies and standards for data sharing across genomic research and healthcare

scientific article published on 10 November 2021

GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA

scientific article published in 2023

IGD: high-performance search for large-scale genomic interval datasets

scientific article published on 26 December 2020

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

scientific article published on 15 October 2012

Identity and compatibility of reference genome resources

scientific article published on 14 May 2021

LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor

scientific article

LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis.

scientific article published in July 2018

Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects

scientific article

MIRA: An R package for DNA methylation-based inference of regulatory activity

scientific article published in March 2018

Mitochondrial genomics in Orthoptera using MOSAS.

scientific article published in June 2010

Multi-Omics of Single Cells: Strategies and Applications

scientific article published on 19 May 2016

Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics

scientific article published on 15 July 2009

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

scientific article

PEPATAC: An optimized pipeline for ATAC-seq data analysis with serial alignments

scientific article

PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments

scientific article published on 23 November 2021

PEPPRO: quality control and processing of nascent RNA profiling data

scientific article published on 15 May 2021

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

Predicting cell-type-specific gene expression from regions of open chromatin

scientific article published on September 2012

Quality control and processing of nascent RNA profiling data

scientific article

Refgenie: a reference genome resource manager

scientific article published on 01 February 2020

Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics

scientific article

Single-cell epigenomic variability reveals functional cancer heterogeneity

scientific article published on 24 January 2017

The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space

The Interaction between Base Compositional Heterogeneity and Among-Site Rate Variation in Models of Molecular Evolution

article

The accessible chromatin landscape of the human genome

scientific article

The chromatin accessibility landscape of primary human cancers

scientific article

The second European interdisciplinary Ewing sarcoma research summit--A joint effort to deconstructing the multiple layers of a complex disease

scientific article

When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics

article

simpleCache: R caching for reproducible, distributed, large-scale projects

scientific article published on 11 January 2018

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