Dashnow Lab

Research

Highlighted

STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci
STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci
Laurel Hiatt, Ben Weisburd, Egor Dolzhenko, Grace E. VanNoy, Edibe Nehir Kurtas, Heidi L. Rehm, Aaron Quinlan, Harriet Dashnow
Cold Spring Harbor Laboratory   ·   21 May 2024   ·   doi:10.1101/2024.05.21.24307682
Paper
Website
GitHub
short reads STRs resource database population variation

All

2024

Defining a tandem repeat catalog and variation clusters for genome-wide analyses and population databases
Defining a tandem repeat catalog and variation clusters for genome-wide analyses and population databases
Ben Weisburd, Egor Dolzhenko, Mark F. Bennett, Matt C. Danzi, Adam English, ..., Fritz J. Sedlazeck, Melissa Gymrek, Harriet Dashnow, Michael A. Eberle, Heidi L. Rehm
Cold Spring Harbor Laboratory   ·   05 Oct 2024   ·   doi:10.1101/2024.10.04.615514
Paper
long reads short reads
The Platinum Pedigree: A long-read benchmark for genetic variants
The Platinum Pedigree: A long-read benchmark for genetic variants
Zev Kronenberg, Cillian Nolan, Tom Mokveld, William J Rowell, Sangjin Lee, ..., Lynn B. Jorde, Deborah W Neklason, Aaron Quinlan, Evan Eichler, Michael A Eberle
Cold Spring Harbor Laboratory   ·   03 Oct 2024   ·   doi:10.1101/2024.10.02.616333
genome annotation STRs VNTRs
High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
Jonas A Gustafson, Sophia B Gibson, Nikhita Damaraju, Miranda PG Zalusky, Kendra Hoekzema, ..., Michael C Zody, Matthew Loose, Miten Jain, Evan E Eichler, Danny E. Miller
Genome Research   ·   02 Oct 2024   ·   doi:10.1101/gr.279273.124
Paper
STRs long reads
A familial, telomere-to-telomere reference for human <i>de novo</i> mutation and recombination from a four-generation pedigree
A familial, telomere-to-telomere reference for human de novo mutation and recombination from a four-generation pedigree
David Porubsky, Harriet Dashnow, Thomas A. Sasani, Glennis A. Logsdon, Pille Hallast, ..., Deborah W. Neklason, Lynn B. Jorde, Aaron R. Quinlan, Michael A. Eberle, Evan E. Eichler
Cold Spring Harbor Laboratory   ·   05 Aug 2024   ·   doi:10.1101/2024.08.05.606142
GitHub
Paper
long reads short reads STRs VNTRs mutation rates
TRGT-denovo: accurate detection of <i>de novo</i> tandem repeat mutations
TRGT-denovo: accurate detection of de novo tandem repeat mutations
T. Mokveld, E. Dolzhenko, H. Dashnow, T. J. Nicholas, T. Sasani, ..., A. J. Sharp, A. R. Quinlan, C. Gilissen, A. Hoischen, M. A. Eberle
Cold Spring Harbor Laboratory   ·   19 Jul 2024   ·   doi:10.1101/2024.07.16.600745
GitHub
long reads STRs VNTRs
Spotted with AuDHD: Seeing Yourself in a Mentor Who Sees You.
Spotted with AuDHD: Seeing Yourself in a Mentor Who Sees You.
Laurel Hiatt
EdArXiv   ·   01 Jun 2024   ·   doi:10.35542/osf.io/pys86
Paper
Essay Mentorship Careers Neurodiversity
STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci
STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci
Laurel Hiatt, Ben Weisburd, Egor Dolzhenko, Grace E. VanNoy, Edibe Nehir Kurtas, Heidi L. Rehm, Aaron Quinlan, Harriet Dashnow
Cold Spring Harbor Laboratory   ·   21 May 2024   ·   doi:10.1101/2024.05.21.24307682
Paper
Website
GitHub
short reads STRs resource database population variation
Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation
Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation
Jonas A Gustafson, Sophia B Gibson, Nikhita Damaraju, Miranda PG Zalusky, Kendra Hoekzema, ..., Michael C Zody, Matthew Loose, Miten Jain, Evan E Eichler, Danny E Miller
Cold Spring Harbor Laboratory   ·   07 Mar 2024   ·   doi:10.1101/2024.03.05.24303792
Sequencing and characterizing short tandem repeats in the human genome
Sequencing and characterizing short tandem repeats in the human genome
Hope A. Tanudisastro, Ira W. Deveson, Harriet Dashnow, Daniel G. MacArthur
Nature Reviews Genetics   ·   16 Feb 2024   ·   doi:10.1038/s41576-024-00692-3
Paper
STRs long reads short reads review
Characterization and visualization of tandem repeats at genome scale
Characterization and visualization of tandem repeats at genome scale
Egor Dolzhenko, Adam English, Harriet Dashnow, Guilherme De Sena Brandine, Tom Mokveld, ..., Stephan Zuchner, Tomi Pastinen, Aaron R. Quinlan, Fritz J. Sedlazeck, Michael A. Eberle
Nature Biotechnology   ·   02 Jan 2024   ·   doi:10.1038/s41587-023-02057-3
Paper
GitHub
long reads STRs VNTRs

2022

STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci
STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci
Harriet Dashnow, Brent S. Pedersen, Laurel Hiatt, Joe Brown, Sarah J. Beecroft, ..., Miriam J. Rodrigues, Mark Davis, Heather C. Mefford, Nigel G. Laing, Aaron R. Quinlan
Genome Biology   ·   14 Dec 2022   ·   doi:10.1186/s13059-022-02826-4
short reads STRs

2021

Effective variant filtering and expected candidate variant yield in studies of rare human disease
Effective variant filtering and expected candidate variant yield in studies of rare human disease
Brent S. Pedersen, Joe M. Brown, Harriet Dashnow, Amelia D. Wallace, Matt Velinder, ..., Tatiana Tvrdik, Rong Mao, D. Hunter Best, Pinar Bayrak-Toydemir, Aaron R. Quinlan
npj Genomic Medicine   ·   15 Jul 2021   ·   doi:10.1038/s41525-021-00227-3

2019

Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software
Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software
Peter Georgeson, Anna Syme, Clare Sloggett, Jessica Chung, Harriet Dashnow, Michael Milton, Andrew Lonsdale, David Powell, Torsten Seemann, Bernard Pope
GigaScience   ·   01 Sep 2019   ·   doi:10.1093/gigascience/giz109
GitHub
Pooled-parent exome sequencing to prioritise <i>de novo</i> variants in genetic disease
Pooled-parent exome sequencing to prioritise de novo variants in genetic disease
Harriet Dashnow, Katrina M. Bell, Zornitza Stark, Tiong Y. Tan, Susan M. White, Alicia Oshlack
Cold Spring Harbor Laboratory   ·   07 Apr 2019   ·   doi:10.1101/601740

2018

STRetch: detecting and discovering pathogenic short tandem repeat expansions
STRetch: detecting and discovering pathogenic short tandem repeat expansions
Harriet Dashnow, Monkol Lek, Belinda Phipson, Andreas Halman, Simon Sadedin, ..., Phillipa Lamont, Joshua S. Clayton, Nigel G. Laing, Daniel G. MacArthur, Alicia Oshlack
Genome Biology   ·   21 Aug 2018   ·   doi:10.1186/s13059-018-1505-2
GitHub

2017

Elegant SciPy
Elegant SciPy
Juan Nunez-Iglesias, Stéfan van der Walt, Harriet Dashnow
O'Reilly Media, Inc.   ·   08 Nov 2017   ·   isbn:9781491922941
A clinically driven variant prioritization framework outperforms purely computational approaches for the diagnostic analysis of singleton WES data
A clinically driven variant prioritization framework outperforms purely computational approaches for the diagnostic analysis of singleton WES data
Zornitza Stark, Harriet Dashnow, Sebastian Lunke, Tiong Y Tan, Alison Yeung, ..., Ivan Macciocca, Clara Gaff, Alicia Oshlack, Susan M White, Paul A James
European Journal of Human Genetics   ·   23 Aug 2017   ·   doi:10.1038/ejhg.2017.123
Melbourne Genomics variant prioritisation

2016

Ten Simple Rules for a Bioinformatics Journal Club
Ten Simple Rules for a Bioinformatics Journal Club
Andrew Lonsdale, Jocelyn Sietsma Penington, Timothy Rice, Michael Walker, Harriet Dashnow
PLOS Computational Biology   ·   28 Jan 2016   ·   doi:10.1371/journal.pcbi.1004526

2015

Cpipe: a shared variant detection pipeline designed for diagnostic settings
Cpipe: a shared variant detection pipeline designed for diagnostic settings
Simon P. Sadedin, Harriet Dashnow, Paul A. James, Melanie Bahlo, Denis C. Bauer, ..., Susan M. White, Graham Taylor, Clara Gaff, Alicia Oshlack, Natalie P. Thorne
Genome Medicine   ·   10 Jul 2015   ·   doi:10.1186/s13073-015-0191-x

2014

Data Interlocking: Coupling Analytics to the Data
Data Interlocking: Coupling Analytics to the Data
Yousef Kowsar, Harriet Dashnow, Andrew Lonie
2014 IEEE/ACM 7th International Conference on Utility and Cloud Computing   ·   01 Dec 2014   ·   doi:10.1109/ucc.2014.113
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
Michael Inouye, Harriet Dashnow, Lesley-Ann Raven, Mark B Schultz, Bernard J Pope, Takehiro Tomita, Justin Zobel, Kathryn E Holt
Genome Medicine   ·   20 Nov 2014   ·   doi:10.1186/s13073-014-0090-6
Ten Simple Rules for Writing a PLOS Ten Simple Rules Article
Ten Simple Rules for Writing a PLOS Ten Simple Rules Article
Harriet Dashnow, Andrew Lonsdale, Philip E. Bourne
PLoS Computational Biology   ·   23 Oct 2014   ·   doi:10.1371/journal.pcbi.1003858

2012

Development of Transgenic Mice Containing an Introduced Stop Codon on the Human Methylmalonyl-CoA Mutase Locus
Development of Transgenic Mice Containing an Introduced Stop Codon on the Human Methylmalonyl-CoA Mutase Locus
Nicole E. Buck, Harriet Dashnow, James J. Pitt, Leonie R. Wood, Heidi L. Peters
PLoS ONE   ·   14 Sep 2012   ·   doi:10.1371/journal.pone.0044974