Constructing founder sets under allelic and non-allelic homologous recombination

Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders

(2022) David Porubsky et al.   CELL

The Human Pangenome Project: a global resource to map genomic diversity

(2022) Ting Wang et al.   NATURE

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

Segmental duplications and their variation in a complete human genome

(2022) Mitchell R. Vollger et al.   SCIENCE

MBG: Minimizer-based Sparse de Bruijn Graph Construction

(2021) Mikko Rautiainen et al.   BIOINFORMATICS

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

(2021) Peter Ebert et al.   SCIENCE

Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies

(2021) Xuefang Zhao et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Founder reconstruction enables scalable and seamless pangenomic analysis

(2021) Tuukka Norri et al.   BIOINFORMATICS

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

(2020) David Porubsky et al.   NATURE BIOTECHNOLOGY

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

(2019) Mark J. P. Chaisson et al.   Nature Communications

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

(2018) Fritz J. Sedlazeck et al.   NATURE REVIEWS GENETICS

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes

(2015) Mingfu Shao et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT)

(2014) R. Durbin   BIOINFORMATICS

Large neighbourhood search algorithms for the founder sequence reconstruction problem

(2011) Andrea Roli et al.   COMPUTERS & OPERATIONS RESEARCH

The origins and impact of primate segmental duplications

(2009) Tomas Marques-Bonet et al.   TRENDS IN GENETICS

Estimating the Ancestral Recombinations Graph (ARG) as Compatible Networks of SNP Patterns

(2008) Laxmi Parida et al.   JOURNAL OF COMPUTATIONAL BIOLOGY