Harriet Dashnow, PhD

Professional Titles

• Assistant Professor

Research Interests

I develop computational methods and workflows to increase the diagnosis of rare diseases with a special focus on Tandem Repeat loci. I partner with clinicians and researchers to analyze patient genomes at scale and establish genetic diagnoses. Learn more on my lab website: dashnowlab.org

Publications

• Tanudisastro HA, Deveson IW, Dashnow H, MacArthur DG. Sequencing and characterizing short tandem repeats in the human genome. Nat Rev Genet. 2024 Jul;25(7):460-475. PubMed PMID: 38366034
• Lonsdale A, Sietsma Penington J, Rice T, Walker M, Dashnow H. Ten Simple Rules for a Bioinformatics Journal Club. PLoS Comput Biol. 2016 Jan;12(1):e1004526. PubMed PMID: 26820645
• Dolzhenko E, English A, Dashnow H, De Sena Brandine G, Mokveld T, Rowell WJ, Karniski C, Kronenberg Z, Danzi MC, Cheung WA, Bi C, Farrow E, Wenger A, Chua KP, Martínez-Cerdeño V, Bartley TD, Jin P, Nelson DL, Zuchner S, Pastinen T, Quinlan AR, Sedlazeck FJ, Eberle MA. Characterization and visualization of tandem repeats at genome scale. Nat Biotechnol. 2024 Jan 2. [Epub ahead of print] PubMed PMID: 38168995
• Dashnow H, Lonsdale A, Bourne PE. Ten simple rules for writing a PLOS ten simple rules article. PLoS Comput Biol. 2014 Oct;10(10):e1003858. PubMed PMID: 25340653
• Gustafson JA, Gibson SB, Damaraju N, Zalusky MPG, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, Anderson ZB, Storz SHR, Ward SA, Sinha M, Gonzaga-Jauregui C, Clarke WE, Basile AO, Corvelo A, Reeves C, Helland A, Musunuri RL, Revsine M, Patterson KE, Paschal CR, Zakarian C, Goodwin S, Jensen TD, Robb E, McCombie WR, Sedlazeck FJ, Zook JM, Montgomery SB, Garrison E, Kolmogorov M, Schatz MC, McLaughlin RN Jr, Dashnow H, Zody MC, Loose M, Jain M, Eichler EE, Miller DE. High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation. Genome Res. 2024 Nov 20;34(11):2061-2073. PubMed PMID: 39358015
• Porubsky D, Dashnow H, Sasani TA, Logsdon GA, Hallast P, Noyes MD, Kronenberg ZN, Mokveld T, Koundinya N, Nolan C, Steely CJ, Guarracino A, Dolzhenko E, Harvey WT, Rowell WJ, Grigorev K, Nicholas TJ, Oshima KK, Lin J, Ebert P, Watkins WS, Leung TY, Hanlon VCT, McGee S, Pedersen BS, Goldberg ME, Happ HC, Jeong H, Munson KM, Hoekzema K, Chan DD, Wang Y, Knuth J, Garcia GH, Fanslow C, Lambert C, Lee C, Smith JD, Levy S, Mason CE, Garrison E, Lansdorp PM, Neklason DW, Jorde LB, Quinlan AR, Eberle MA, Eichler EE. A familial, telomere-to-telomere reference for human de novo mutation and recombination from a four-generation pedigree. bioRxiv. 2024 Aug 5. PubMed PMID: 39149261
• Mokveld T, Dolzhenko E, Dashnow H, Nicholas TJ, Sasani T, van der Sanden B, Jadhav B, Pedersen B, Kronenberg Z, Tucci A, Sharp AJ, Quinlan AR, Gilissen C, Hoischen A, Eberle MA. TRGT-denovo: accurate detection of de novo tandem repeat mutations. bioRxiv. 2024 Jul 19. PubMed PMID: 39071386
• Gustafson JA, Gibson SB, Damaraju N, Zalusky MP, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, Anderson Z, Storz SH, Ward SA, Sinha M, Gonzaga-Jauregui C, Clarke WE, Basile AO, Corvelo A, Reeves C, Helland A, Musunuri RL, Revsine M, Patterson KE, Paschal CR, Zakarian C, Goodwin S, Jensen TD, Robb E, McCombie WR, Sedlazeck FJ, Zook JM, Montgomery SB, Garrison E, Kolmogorov M, Schatz MC, McLaughlin RN Jr, Dashnow H, Zody MC, Loose M, Jain M, Eichler EE, Miller DE. Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation. medRxiv. 2024 Mar 7. PubMed PMID: 38496498
• Hiatt L, Weisburd B, Dolzhenko E, VanNoy GE, Kurtas EN, Rehm HL, Quinlan A, Dashnow H. STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci. medRxiv. 2024 May 21. PubMed PMID: 38826469
• Tanudisastro HA, Deveson IW, Dashnow H, MacArthur DG. Sequencing and characterizing short tandem repeats in the human genome. Nat Rev Genet. 2024 Jul;25(7):460-475. PubMed PMID: 38366034
• Dashnow H, Pedersen BS, Hiatt L, Brown J, Beecroft SJ, Ravenscroft G, LaCroix AJ, Lamont P, Roxburgh RH, Rodrigues MJ, Davis M, Mefford HC, Laing NG, Quinlan AR. STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci. Genome Biol. 2022 Dec 14;23(1):257. PubMed PMID: 36517892
• Dashnow H, Lek M, Phipson B, Halman A, Sadedin S, Lonsdale A, Davis M, Lamont P, Clayton JS, Laing NG, MacArthur DG, Oshlack A. STRetch: detecting and discovering pathogenic short tandem repeat expansions. Genome Biol. 2018 Aug 21;19(1):121. PubMed PMID: 30129428
• Dolzhenko E, English A, Dashnow H, De Sena Brandine G, Mokveld T, Rowell WJ, Karniski C, Kronenberg Z, Danzi MC, Cheung WA, Bi C, Farrow E, Wenger A, Chua KP, Martínez-Cerdeño V, Bartley TD, Jin P, Nelson DL, Zuchner S, Pastinen T, Quinlan AR, Sedlazeck FJ, Eberle MA. Characterization and visualization of tandem repeats at genome scale. Nat Biotechnol. 2024 Oct;42(10):1606-1614. PubMed PMID: 38168995
• Tanudisastro, H. A., Cuomo, A. S., Weisburd, B., Welland, M., Spenceley, E., Franklin, M., ... & MacArthur, D. G. (2024). Polymorphic tandem repeats shape single-cell gene expression across the immune landscape. bioRxiv, 2024-11.
• Weisburd, B., Dolzhenko, E., Bennett, M. F., Danzi, M. C., English, A., Hiatt, L., ... & Rehm, H. L. (2024). Defining a tandem repeat catalog and variation clusters for genome-wide analyses and population databases. bioRxiv, 2024-10.
• Kronenberg, Z., Nolan, C., Mokveld, T., Rowell, W. J., Lee, S., Dolzhenko, E., ... & Eberle, M. A. (2024). The Platinum Pedigree: A long-read benchmark for genetic variants. bioRxiv, 2024-10.
• Hiatt L, Weisburd B, Dolzhenko E, VanNoy GE, Kurtas EN, Rehm HL, Quinlan A, Dashnow H. STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci. medRxiv. 2024 May 21. PubMed PMID: 38826469
• Mokveld T, Dolzhenko E, Dashnow H, Nicholas TJ, Sasani T, van der Sanden B, Jadhav B, Pedersen B, Kronenberg Z, Tucci A, Sharp AJ, Quinlan AR, Gilissen C, Hoischen A, Eberle MA. TRGT-denovo: accurate detection of de novo tandem repeat mutations. bioRxiv. 2024 Jul 19. PubMed PMID: 39071386
• Porubsky D, Dashnow H, Sasani TA, Logsdon GA, Hallast P, Noyes MD, Kronenberg ZN, Mokveld T, Koundinya N, Nolan C, Steely CJ, Guarracino A, Dolzhenko E, Harvey WT, Rowell WJ, Grigorev K, Nicholas TJ, Oshima KK, Lin J, Ebert P, Watkins WS, Leung TY, Hanlon VCT, McGee S, Pedersen BS, Goldberg ME, Happ HC, Jeong H, Munson KM, Hoekzema K, Chan DD, Wang Y, Knuth J, Garcia GH, Fanslow C, Lambert C, Lee C, Smith JD, Levy S, Mason CE, Garrison E, Lansdorp PM, Neklason DW, Jorde LB, Quinlan AR, Eberle MA, Eichler EE. A familial, telomere-to-telomere reference for human de novo mutation and recombination from a four-generation pedigree. bioRxiv. 2024 Aug 5. PubMed PMID: 39149261
• Pedersen BS, Brown JM, Dashnow H, Wallace AD, Velinder M, Tristani-Firouzi M, Schiffman JD, Tvrdik T, Mao R, Best DH, Bayrak-Toydemir P, Quinlan AR. Effective variant filtering and expected candidate variant yield in studies of rare human disease. NPJ Genom Med. 2021 Jul 15;6(1):60. PubMed PMID: 34267211
• Shere H, Weijer L, Dashnow H, Moreno LE, Foxworthy Scott S, Baker H. Chronic Lactation Insufficiency Is a Public Health Issue: Commentary on "We Need Patient-Centered Research in Breastfeeding Medicine" by Stuebe. Breastfeed Med 2021;16:349-350. Breastfeed Med. 2021 Dec;16(12):933-934. PubMed PMID: 34403595
• Georgeson P, Syme A, Sloggett C, Chung J, Dashnow H, Milton M, Lonsdale A, Powell D, Seemann T, Pope B. Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software. Gigascience. 2019 Sep 1;8(9). PubMed PMID: 31544213
• Stark Z, Dashnow H, Lunke S, Tan TY, Yeung A, Sadedin S, Thorne N, Macciocca I, Gaff C, Oshlack A, White SM, James PA. A clinically driven variant prioritization framework outperforms purely computational approaches for the diagnostic analysis of singleton WES data. Eur J Hum Genet. 2017 Nov;25(11):1268-1272. PubMed PMID: 28832562
• Sadedin SP, Dashnow H, James PA, Bahlo M, Bauer DC, Lonie A, Lunke S, Macciocca I, Ross JP, Siemering KR, Stark Z, White SM, Taylor G, Gaff C, Oshlack A, Thorne NP. Cpipe: a shared variant detection pipeline designed for diagnostic settings. Genome Med. 2015;7(1):68. PubMed PMID: 26217397
• Inouye M, Dashnow H, Raven LA, Schultz MB, Pope BJ, Tomita T, Zobel J, Holt KE. SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Med. 2014;6(11):90. PubMed PMID: 25422674
• Buck NE, Dashnow H, Pitt JJ, Wood LR, Peters HL. Development of transgenic mice containing an introduced stop codon on the human methylmalonyl-CoA mutase locus. PLoS One. 2012;7(9):e44974. PubMed PMID: 23024777