User profiles for S. Koren

Sergey Koren

- Verified email at nih.gov - Cited by 50788

Seth Koren

- Verified email at nd.edu - Cited by 784

[HTML][HTML] Assembly algorithms for next-generation sequencing data

JR Miller, S Koren, G Sutton - Genomics, 2010 - Elsevier
The emergence of next-generation sequencing platforms led to resurgence of research in
whole-genome shotgun assembly algorithms and software. DNA sequencing data from the …

[HTML][HTML] One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly

S Koren, AM Phillippy - Current opinion in microbiology, 2015 - Elsevier
… Author links open overlay panel Sergey Koren , Adam M Phillippy … As introduced by Koren
et al. [34 •• ], long-read correction involves mapping multiple reads to a single long read to …

The muon Smasher's guide

…, IG Garcia, S Homiller, S Koren… - Reports on Progress …, 2022 - iopscience.iop.org
We lay out a comprehensive physics case for a future high-energy muon collider, exploring
a range of collision energies (from 1 to 100 TeV) and luminosities. We highlight the …

The complete sequence of a human genome

S Nurk, S Koren, A Rhie, M Rautiainen, AV Bzikadze… - Science, 2022 - science.org
Since its initial release in 2000, the human reference genome has covered only the
euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. …

[HTML][HTML] Towards complete and error-free genome assemblies of all vertebrate species

…, O Fedrigo, J Damas, G Formenti, S Koren… - Nature, 2021 - nature.com
High-quality and complete reference genome assemblies are fundamental for the application
of genomics to biology, disease, and biodiversity conservation. However, such assemblies …

[HTML][HTML] Nanopore sequencing and assembly of a human genome with ultra-long reads

M Jain, S Koren, KH Miga, J Quick, AC Rand… - Nature …, 2018 - nature.com
We report the sequencing and assembly of a reference genome for the human GM12878
Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. …

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

S Koren, BP Walenz, K Berlin, JR Miller… - Genome …, 2017 - genome.cshlp.org
… a set Γ of s hash functions is defined for a sketch S of size s. Each sketch entry S i is defined
as … The resulting set of s minimum-valued k-mers, or min-mers, comprise the sketch. Given a …

[HTML][HTML] A draft human pangenome reference

…, A Kolesnikov, JO Korbel, J Kordosky, S Koren… - Nature, 2023 - nature.com
Here the Human Pangenome Reference Consortium presents a first draft of the human
pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of …

[HTML][HTML] Mash: fast genome and metagenome distance estimation using MinHash

…, P Melsted, AB Mallonee, NH Bergman, S Koren… - Genome biology, 2016 - Springer
… MinHash sketches S(A) and S(B) of size s = 5 are shown for A and B, comprising the five …
S(A) and S(B) to recover the five smallest hash values overall for A∪B (crossed circles) yields S

[HTML][HTML] Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies

A Rhie, BP Walenz, S Koren, AM Phillippy - Genome biology, 2020 - Springer
… In the following sections, we describe how Merqury’s statistics and plots can be used to … We
note that Merqury’s methods are general and would be compatible with any reasonable high-…