Search filters

List of works by Aaron R Quinlan

A map of constrained coding regions in the human genome

scientific article published on 10 December 2018

A novel IFITM5 mutation in severe atypical osteogenesis imperfecta type VI impairs osteoblast production of pigment epithelium-derived factor

scientific article

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer.

scientific article

An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder

scientific article published on 26 April 2018

BEDTools: The Swiss-Army Tool for Genome Feature Analysis.

scientific article

BEDTools: a flexible suite of utilities for comparing genomic features

scientific article

BamTools: a C++ API and toolkit for analyzing and managing BAM files

scientific article

Binary Interval Search: a scalable algorithm for counting interval intersections

scientific article

Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms

scientific article

CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing

scientific article published on 08 April 2021

Cas9-chromatin binding information enables more accurate CRISPR off-target prediction.

scientific article

Characterizing complex structural variation in germline and somatic genomes

scientific article

Coexpression patterns define epigenetic regulators associated with neurological dysfunction

scientific article published on 11 March 2019

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

scientific article published in July 2018

Combating subclonal evolution of resistant cancer phenotypes

scientific article published in November 2017

Copy number variation detection and genotyping from exome sequence data

scientific article

Detection and interpretation of genomic structural variation in mammals

scientific article

Efficient genotype compression and analysis of large genetic-variation data sets.

scientific article

Erratum: A reference bacterial genome dataset generated on the MinION(TM) portable single-molecule nanopore sequencer

scientific article published on 13 February 2015

Evidence for two independent associations with type 1 diabetes at the 12q13 locus

scientific article

Extending reference assembly models

scientific article

Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers

scientific article

Fine-mapping and functional studies highlight potential causal variants for rheumatoid arthritis and type 1 diabetes

scientific article published on 17 September 2018

Fine-mapping identifies causal variants for RA and T1D in DNASE1L3, SIRPG, MEG3, TNFAIP3 and CD28/CTLA4 loci

GEMINI: integrative exploration of genetic variation and genome annotations

scientific article

GIGGLE: a search engine for large-scale integrated genome analysis.

scientific article published on 8 January 2018

Genetics of systemic lupus erythematosus: immune responses and end organ resistance to damage

scientific article

Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming

scientific article

Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder

scientific article published on 01 December 2018

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

scientific article

Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data

scientific article published on 12 April 2021

Homozygous mutation of MTPAP causes cellular radiosensitivity and persistent DNA double-strand breaks

scientific article

Indexcov: fast coverage quality control for whole-genome sequencing

scientific article published on 18 September 2017

LUMPY: a probabilistic framework for structural variant discovery.

scientific article

Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays

article

Nanopore sequencing and assembly of a human genome with ultra-long reads.

scientific article published on 29 January 2018

OncoGEMINI: software for investigating tumor variants from multiple biopsies with integrated cancer annotations

scientific article published on 26 March 2021

Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster

scientific article

Population-based structural variation discovery with Hydra-Multi.

scientific article

Poretools: a toolkit for analyzing nanopore sequence data

scientific article

Primer-site SNPs mask mutations

scientific article published in March 2007

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

scientific article

Pyrobayes: an improved base caller for SNP discovery in pyrosequences

scientific article published on 13 January 2008

Rapid whole-genome mutational profiling using next-generation sequencing technologies

scientific article published on 4 September 2008

Rare and Coding Region Genetic Variants Associated With Risk of Ischemic Stroke: The NHLBI Exome Sequence Project

scientific article

SV-plaudit: A cloud-based framework for manually curating thousands of structural variants.

scientific article published in July 2018

SpeedSeq: ultra-fast personal genome analysis and interpretation

scientific article

SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization

scientific article

Targeted Deep Sequencing in Multiple-Affected Sibships of European Ancestry Identifies Rare Deleterious Variants in PTPN22 That Confer Risk for Type 1 Diabetes

scientific article

Vcfanno: fast, flexible annotation of genetic variants

scientific article published on June 2016

Who's Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy

scientific article published on 30 January 2017

Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy

article

Whole-genome sequencing and variant discovery in C. elegans.

scientific article

cyvcf2: fast, flexible variant analysis with Python.

scientific article

hts-nim: scripting high-performance genomic analyses

scientific article published on 01 October 2018

mosdepth: quick coverage calculation for genomes and exomes

scientific article published on 31 October 2017

Paulina is supported by:

About Paulina

Help