Reducing noise and stutter in short tandem repeat loci with unique molecular identifiers

UMI-VarCal: a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries

(2020) Vincent Sater et al.   BIOINFORMATICS

ExpansionHunter: A sequence-graph based tool to analyze variation in short tandem repeat regions

(2019) Egor Dolzhenko et al.   BIOINFORMATICS

A novel phylogenetic approach for de novo discovery of putative nuclear mitochondrial (pNumt) haplotypes

(2019) Utpal Smart et al.   Forensic Science International-Genetics

Ultra-deep massively parallel sequencing with unique molecular identifier tagging achieves comparable performance to droplet digital PCR for detection and quantification of circulating tumor DNA from lung cancer patients

(2019) Le Son Tran et al.   PLoS One

OUP accepted manuscript

(2018)   BIOINFORMATICS

Duplex Proximity Sequencing (Pro-Seq): A method to improve DNA sequencing accuracy without the cost of molecular barcoding redundancy

(2018) Joel Pel et al.   PLoS One

Probabilistic genotyping software: An overview

(2018) Michael D. Coble et al.   Forensic Science International-Genetics

STRait Razor v2s: Advancing sequence-based STR allele reporting and beyond to other marker systems

(2017) Jonathan L. King et al.   Forensic Science International-Genetics

Fast STR allele identification with STRait Razor 3.0

(2017) August E. Woerner et al.   Forensic Science International-Genetics

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Genome-wide profiling of heritable and de novo STR variations

(2017) Thomas Willems et al.   NATURE METHODS

Introduction of the Python script STRinNGS for analysis of STR regions in FASTQ or BAM files and expansion of the Danish STR sequence database to 11 STRs

(2016) Susanne L. Friis et al.   Forensic Science International-Genetics

Characterization of genetic sequence variation of 58 STR loci in four major population groups

(2016) Nicole M.M. Novroski et al.   Forensic Science International-Genetics

OutLyzer: software for extracting low-allele-frequency tumor mutations from sequencing background noise in clinical practice

(2016) Etienne Muller et al.   Oncotarget

DeepSNVMiner: a sequence analysis tool to detect emergent, rare mutations in subsets of cell populations

(2016) T. Daniel Andrews et al.   PeerJ

Reducing amplification artifacts in high multiplex amplicon sequencing by using molecular barcodes

(2015) Quan Peng et al.   BMC GENOMICS

STRait Razor v2.0: The improved STR Allele Identification Tool – Razor

(2015) David H. Warshauer et al.   Forensic Science International-Genetics

Building Predictive Models inRUsing thecaretPackage

(2015) Max Kuhn   Journal of Statistical Software

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes

(2014) Seyed Yahya Anvar et al.   BIOINFORMATICS

pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires

(2014) Jason A. Vander Heiden et al.   BIOINFORMATICS

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

STRait Razor: A length-based forensic STR allele-calling tool for use with second generation sequencing data

(2013) David H. Warshauer et al.   Forensic Science International-Genetics

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

lobSTR: A short tandem repeat profiler for personal genomes

(2012) Melissa Gymrek et al.   GENOME RESEARCH

Detection of ultra-rare mutations by next-generation sequencing

(2012) M. W. Schmitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A stochastic model of the processes in PCR based amplification of STR DNA in forensic applications

(2011) Jos Weusten et al.   Forensic Science International-Genetics

Characterising stutter in forensic STR multiplexes

(2011) Clare Brookes et al.   Forensic Science International-Genetics

A method for counting PCR template molecules with application to next-generation sequencing

(2011) J. A. Casbon et al.   NUCLEIC ACIDS RESEARCH

Detection and quantification of rare mutations with massively parallel sequencing

(2011) I. Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA