Personal information

No personal information available

Activities

Collapse all

Employment (1)

University of Washington Department of Genome Sciences: Seattle, WA, US

2018-08-01 to present
Employment
Source: Self-asserted source
David Porubsky

Works (35)

Independent expansion, selection, and hypervariability of theTBC1D3gene family in humans

Genome Research
2024-11 | Journal article
DOI: 10.1101/gr.279299.124
Contributors: Xavi Guitart; David Porubsky; DongAhn Yoo; Max L. Dougherty; Philip C. Dishuck; Katherine M. Munson; Alexandra P. Lewis; Kendra Hoekzema; Jordan Knuth; Stephen Chang et al.
Source: check_circle
Crossref

Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing

Genome Biology
2024-10-10 | Journal article
DOI: 10.1186/s13059-024-03409-1
Contributors: Mir Henglin; Maryam Ghareghani; William T. Harvey; David Porubsky; Sergey Koren; Evan E. Eichler; Peter Ebert; Tobias Marschall
Source: check_circle
Crossref

Complex genetic variation in nearly complete human genomes

2024-09-25 | Preprint
DOI: 10.1101/2024.09.24.614721
Contributors: Glennis A. Logsdon; Peter Ebert; Peter A. Audano; Mark Loftus; David Porubsky; Jana Ebler; Feyza Yilmaz; Pille Hallast; Timofey Prodanov; DongAhn Yoo et al.
Source: check_circle
Crossref

SVbyEye: A visual tool to characterize structural variation among whole-genome assemblies

2024-09-14 | Preprint
DOI: 10.1101/2024.09.11.612418
Contributors: David Porubsky; Xavi Guitart; DongAhn Yoo; Philip C. Dishuck; William T. Harvey; Evan E. Eichler
Source: check_circle
Crossref

A familial, telomere-to-telomere reference for humande novomutation and recombination from a four-generation pedigree

2024-08-05 | Preprint
DOI: 10.1101/2024.08.05.606142
Contributors: David Porubsky; Harriet Dashnow; Thomas A. Sasani; Glennis A. Logsdon; Pille Hallast; Michelle D. Noyes; Zev N. Kronenberg; Tom Mokveld; Nidhi Koundinya; Cillian Nolan et al.
Source: check_circle
Crossref

The variation and evolution of complete human centromeres

Nature
2024-05-02 | Journal article
DOI: 10.1038/s41586-024-07278-3
Contributors: Glennis A. Logsdon; Allison N. Rozanski; Fedor Ryabov; Tamara Potapova; Valery A. Shepelev; Claudia R. Catacchio; David Porubsky; Yafei Mao; DongAhn Yoo; Mikko Rautiainen et al.
Source: check_circle
Crossref

Independent expansion, selection and hypervariability of theTBC1D3gene family in humans

2024-03-13 | Preprint
DOI: 10.1101/2024.03.12.584650
Contributors: Xavi Guitart; David Porubsky; DongAhn Yoo; Max L. Dougherty; Philip C. Dishuck; Katherine M. Munson; Alexandra P. Lewis; Kendra Hoekzema; Jordan Knuth; Stephen Chang et al.
Source: check_circle
Crossref

Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing

2024-02-16 | Preprint
DOI: 10.1101/2024.02.15.580432
Contributors: Mir Henglin; Maryam Ghareghani; William Harvey; David Porubsky; Sergey Koren; Evan E. Eichler; Peter Ebert; Tobias Marschall
Source: check_circle
Crossref

Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall

Genome Research
2023-12 | Journal article
DOI: 10.1101/gr.278070.123
Contributors: William T. Harvey; Peter Ebert; Jana Ebler; Peter A. Audano; Katherine M. Munson; Kendra Hoekzema; David Porubsky; Christine R. Beck; Tobias Marschall; Kiran Garimella et al.
Source: check_circle
Crossref

Telomere-to-telomere assembly of diploid chromosomes with Verkko

Nature Biotechnology
2023-10 | Journal article
DOI: 10.1038/s41587-023-01662-6
Contributors: Mikko Rautiainen; Sergey Nurk; Brian P. Walenz; Glennis A. Logsdon; David Porubsky; Arang Rhie; Evan E. Eichler; Adam M. Phillippy; Sergey Koren
Source: check_circle
Crossref

Structural Variation Evolution at the 15q11-q13 Disease-Associated Locus

International Journal of Molecular Sciences
2023-10-31 | Journal article
DOI: 10.3390/ijms242115818
Contributors: Annalisa Paparella; Alberto L’Abbate; Donato Palmisano; Gerardina Chirico; David Porubsky; Claudia R. Catacchio; Mario Ventura; Evan E. Eichler; Flavia A. M. Maggiolini; Francesca Antonacci
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Functional analysis of structural variants in single cells using Strand-seq

Nature Biotechnology
2023-06 | Journal article
DOI: 10.1038/s41587-022-01551-4
Contributors: Hyobin Jeong; Karen Grimes; Kerstin K. Rauwolf; Peter-Martin Bruch; Tobias Rausch; Patrick Hasenfeld; Eva Benito; Tobias Roider; Radhakrishnan Sabarinathan; David Porubsky et al.
Source: check_circle
Crossref

The variation and evolution of complete human centromeres

2023-05-31 | Preprint
DOI: 10.1101/2023.05.30.542849
Contributors: Glennis A. Logsdon; Allison N. Rozanski; Fedor Ryabov; Tamara Potapova; Valery A. Shepelev; Yafei Mao; Mikko Rautiainen; Sergey Koren; Sergey Nurk; David Porubsky et al.
Source: check_circle
Crossref

Whole-genome long-read sequencing downsampling and its effect on variant calling precision and recall

2023-05-04 | Preprint
DOI: 10.1101/2023.05.04.539448
Contributors: William T. Harvey; Peter Ebert; Jana Ebler; Peter A. Audano; Katherine M. Munson; Kendra Hoekzema; David Porubsky; Christine R. Beck; Tobias Marschall; Kiran Garimella et al.
Source: check_circle
Crossref

Gaps and complex structurally variant loci in phased genome assemblies

Genome Research
2023-04 | Journal article
DOI: 10.1101/gr.277334.122
Contributors: David Porubsky; Mitchell R. Vollger; William T. Harvey; Allison N. Rozanski; Peter Ebert; Glenn Hickey; Patrick Hasenfeld; Ashley D. Sanders; Catherine Stober; Jan O. Korbel et al.
Source: check_circle
Crossref

Semi-automated assembly of high-quality diploid human reference genomes

Nature
2022-11-17 | Journal article
DOI: 10.1038/s41586-022-05325-5
Contributors: Erich D. Jarvis; Giulio Formenti; Arang Rhie; Andrea Guarracino; Chentao Yang; Jonathan Wood; Alan Tracey; Francoise Thibaud-Nissen; Mitchell R. Vollger; David Porubsky et al.
Source: check_circle
Crossref

Inversion polymorphism in a complete human genome assembly

2022-10-06 | Preprint
DOI: 10.1101/2022.10.06.511148
Contributors: David Porubsky; William T. Harvey; Allison N. Rozanski; Jana Ebler; Wolfram Höps; Hufsah Ashraf; Patrick Hasenfeld; Benedict Paten; Ashley D. Sanders; Tobias Marschall et al.
Source: check_circle
Crossref

Gaps and complex structurally variant loci in phased genome assemblies

2022-07-06 | Preprint
DOI: 10.1101/2022.07.06.498874
Contributors: David Porubsky; Mitchell R. Vollger; William T. Harvey; Allison N. Rozanski; Peter Ebert; Glenn Hickey; Patrick Hasenfeld; Ashley D. Sanders; Catherine Stober; Jan O. Korbel et al.
Source: check_circle
Crossref

Haplotype-resolved inversion landscape reveals hotspots of mutational recurrence associated with genomic disorders

2021-12-20 | Preprint
DOI: 10.1101/2021.12.20.472354
Contributors: David Porubsky; Wolfram Höps; Hufsah Ashraf; PingHsun Hsieh; Bernardo Rodriguez-Martin; Feyza Yilmaz; Jana Ebler; Pille Hallast; Flavia Angela Maria Maggiolini; William T. Harvey et al.
Source: check_circle
Crossref

A high-quality bonobo genome refines the analysis of hominid evolution

Nature
2021-06-03 | Journal article
DOI: 10.1038/s41586-021-03519-x
Contributors: Yafei Mao; Claudia R. Catacchio; LaDeana W. Hillier; David Porubsky; Ruiyang Li; Arvis Sulovari; Jason D. Fernandes; Francesco Montinaro; David S. Gordon; Jessica M. Storer et al.
Source: check_circle
Crossref

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

Science
2021-04-02 | Journal article
DOI: 10.1126/science.abf7117
Contributors: Peter Ebert; Peter A. Audano; Qihui Zhu; Bernardo Rodriguez-Martin; David Porubsky; Marc Jan Bonder; Arvis Sulovari; Jana Ebler; Weichen Zhou; Rebecca Serra Mari et al.
Source: check_circle
Crossref

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

Nature Biotechnology
2021-03-07 | Journal article
DOI: 10.1038/s41587-020-0719-5
Contributors: David Porubsky; Peter Ebert; Peter A. Audano; Mitchell R. Vollger; William T. Harvey; Pierre Marijon; Jana Ebler; Katherine M. Munson; Melanie Sorensen; Arvis Sulovari et al.
Source: check_circle
Crossref

A fully phased accurate assembly of an individual human genome

2019-11-26 | Other
DOI: 10.1101/855049
Contributors: David Porubsky; Peter Ebert; Peter A. Audano; Mitchell R. Vollger; William T. Harvey; Katherine M. Munson; Melanie Sorensen; Arvis Sulovari; Marina Haukness; Maryam Ghareghani et al.
Source: check_circle
Crossref

Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Nature communications
2019-04-16 | Journal article
DOI: 10.1038/s41467-018-08148-z
PMID: 30992455
PMC: PMC6467913
Source: Self-asserted source
David Porubsky

Strand-seq enables reliable separation of long reads by chromosome via expectation maximization.

Bioinformatics (Oxford, England)
2018-07-01 | Journal article
DOI: 10.1093/bioinformatics/bty290
PMID: 29949971
PMC: PMC6022540
Source: Self-asserted source
David Porubsky

Computational pan-genomics: status, promises and challenges.

Briefings in bioinformatics
2018-01-01 | Journal article
DOI: 10.1093/bib/bbw089
PMID: 27769991
PMC: PMC5862344
Source: Self-asserted source
David Porubsky

Genome-wide mapping of sister chromatid exchange events in single yeast cells using Strand-seq.

eLife
2017-12-12 | Journal article
DOI: 10.7554/eLife.30560
PMID: 29231811
PMC: PMC5734873
Source: Self-asserted source
David Porubsky

Dense and accurate whole-chromosome haplotyping of individual genomes.

Nature communications
2017-11-03 | Journal article
DOI: 10.1038/s41467-017-01389-4
PMID: 29101320
PMC: PMC5670131
Source: Self-asserted source
David Porubsky

Copy number alterations assessed at the single-cell level revealed mono- and polyclonal seeding patterns of distant metastasis in a small-cell lung cancer patient.

Annals of oncology : official journal of the European Society for Medical Oncology
2017-07-01 | Journal article
DOI: 10.1093/annonc/mdx182
PMID: 28419234
Source: Self-asserted source
David Porubsky

Direct chromosome-length haplotyping by single-cell sequencing.

Genome research
2016-09-19 | Journal article
DOI: 10.1101/gr.209841.116
PMID: 27646535
PMC: PMC5088598
Source: Self-asserted source
David Porubsky

Characterizing polymorphic inversions in human genomes by single-cell sequencing.

Genome research
2016-07-29 | Journal article
DOI: 10.1101/gr.201160.115
PMID: 27472961
PMC: PMC5088599
Source: Self-asserted source
David Porubsky

Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies.

Genome biology
2016-05-31 | Journal article
DOI: 10.1186/s13059-016-0971-7
PMID: 27246460
PMC: PMC4888588
Source: Self-asserted source
David Porubsky

Single-cell whole genome sequencing reveals no evidence for common aneuploidy in normal and Alzheimer's disease neurons.

Genome biology
2016-05-31 | Journal article
DOI: 10.1186/s13059-016-0976-2
PMID: 27246599
PMC: PMC4888403
Source: Self-asserted source
David Porubsky

The developmental potential of iPSCs is greatly influenced by reprogramming factor selection.

Cell stem cell
2014-09-01 | Journal article
DOI: 10.1016/j.stem.2014.07.003
PMID: 25192464
PMC: PMC4170792
Source: Self-asserted source
David Porubsky

Spectrum of mutations in gastrointestinal stromal tumor patients - a population-based study from Slovakia.

APMIS : acta pathologica, microbiologica, et immunologica Scandinavica
2012-10-27 | Journal article
DOI: 10.1111/apm.12019
PMID: 23106360
Source: Self-asserted source
David Porubsky

Peer review (1 review for 1 publication/grant)

Review activity for Nature methods. (1)
How many people are using ORCID?