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Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

Nature methods, 2021-11, Vol.18 (11), p.1322

2021

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Haplotype-aware diplotyping from noisy long reads

Genome Biology, 2019-06, Vol.20 (1), p.116-16, Article 116

2019

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Genotyping structural variants in pangenome graphs using the vg toolkit

Genome Biology, 2020-02, Vol.21 (1), p.35-35, Article 35

2020

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Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures

Nature communications, 2021-11, Vol.12 (1), p.6545-6545, Article 6545

2021

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

Nature biotechnology, 2021-03, Vol.39 (3), p.302-308

2021

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High-resolution comparative analysis of great ape genomes

Science (American Association for the Advancement of Science), 2018-06, Vol.360 (6393)

2018

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MinION Analysis and Reference Consortium: Phase 1 data release and analysis

F1000 research, 2015, Vol.4, p.1075-1075

2015

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The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows [version 1; peer review: 2 approved]

F1000 research, 2017, Vol.6, p.52-52

2017

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Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling

eLife, 2022-04, Vol.11

2022

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An average-case sublinear forward algorithm for the haploid Li and Stephens model

Algorithms for molecular biology, 2019-04, Vol.14 (1), p.11-11, Article 11

2019

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Inversion polymorphism in a complete human genome assembly

Genome Biology, 2023-04, Vol.24 (1), p.100-100, Article 100

2023

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A graph extension of the positional Burrows-Wheeler transform and its applications

Algorithms for molecular biology, 2017-07, Vol.12 (1), p.18-18, Article 18

2017

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ProTECT-Prediction of T-Cell Epitopes for Cancer Therapy

Frontiers in immunology, 2020-11, Vol.11, p.483296-483296

2020

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Accurate reconstruction of insertion-deletion histories by statistical phylogenetics

PloS one, 2012-04, Vol.7 (4), p.e34572

2012

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Hydroxymethylation profile of cell-free DNA is a biomarker for early colorectal cancer

Scientific reports, 2022-10, Vol.12 (1), p.16566-16566, Article 16566

2022

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Real-Time Culture-Independent Microbial Profiling Onboard the International Space Station using Nanopore Sequencing

Genes, 2021-01, Vol.12 (1), p.106

2021

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Off Earth Identification of Bacterial Populations Using 16S rDNA Nanopore Sequencing

Genes, 2020-01, Vol.11 (1), p.76

2020

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The Genome of C57BL/6J "Eve", the Mother of the Laboratory Mouse Genome Reference Strain

G3 : genes - genomes - genetics, 2019-06, Vol.9 (6), p.1795-1805

2019

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P821: Long-read sequencing resolves CYP21A2 alleles in congenital adrenal hyperplasia

Genetics in Medicine Open, 2024, Vol.2, p.101732

2024

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The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

Genome Biology, 2016-11, Vol.17 (1), p.239, Article 239

2016

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TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets

BMC genomics, 2018-04, Vol.19 (1), p.238-238, Article 238

2018

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Bridging the rodent to human translational gap: Marmosets as model systems for the study of Alzheimer's disease

Alzheimer's & dementia : translational research & clinical interventions, 2023-07, Vol.9 (3), p.e12417-e12417

2023

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GBZ file format for pangenome graphs

Bioinformatics (Oxford, England), 2022-11, Vol.38 (22), p.5012

2022

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Genome graphs and the evolution of genome inference

Genome research, 2017-05, Vol.27 (5), p.665

2017

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Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

Haplotype-aware diplotyping from noisy long reads

Genotyping structural variants in pangenome graphs using the vg toolkit

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures

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

High-resolution comparative analysis of great ape genomes

MinION Analysis and Reference Consortium: Phase 1 data release and analysis

The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows [version 1; peer review: 2 approved]

Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling

An average-case sublinear forward algorithm for the haploid Li and Stephens model

Inversion polymorphism in a complete human genome assembly

A graph extension of the positional Burrows-Wheeler transform and its applications

ProTECT-Prediction of T-Cell Epitopes for Cancer Therapy

Accurate reconstruction of insertion-deletion histories by statistical phylogenetics

Hydroxymethylation profile of cell-free DNA is a biomarker for early colorectal cancer

Real-Time Culture-Independent Microbial Profiling Onboard the International Space Station using Nanopore Sequencing

Off Earth Identification of Bacterial Populations Using 16S rDNA Nanopore Sequencing

The Genome of C57BL/6J "Eve", the Mother of the Laboratory Mouse Genome Reference Strain

P821: Long-read sequencing resolves CYP21A2 alleles in congenital adrenal hyperplasia

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets

Bridging the rodent to human translational gap: Marmosets as model systems for the study of Alzheimer's disease

GBZ file format for pangenome graphs

Genome graphs and the evolution of genome inference

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