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List of works by Sergey Koren

A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases

A chromosome-scale assembly of the major African malaria vector Anopheles funestus

scholarly article published 10 December 2018

A chromosome-scale assembly of the major African malaria vector Anopheles funestus

scientific article published on 01 June 2019

A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads

scientific article

A draft genome sequence for the Ixodes scapularis cell line, ISE6.

scientific article

A draft human pangenome reference

scientific article published on 10 May 2023

A fast adaptive algorithm for computing whole-genome homology maps

scholarly article by Chirag Jain published in September 2018

A framework for human microbiome research

scientific article

A robust benchmark for detection of germline large deletions and insertions

scientific article published on 15 June 2020

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

scientific article published on 12 August 2019

Aggressive assembly of pyrosequencing reads with mates

scientific article published on 24 October 2008

An algorithm for automated closure during assembly

scientific article

An improved pig reference genome sequence to enable pig genetics and genomics research

scientific article published on 01 June 2020

Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation

scientific article published on 10 January 2018

Assemblathon 1: a competitive assessment of de novo short read assembly methods

scientific article

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

scientific article

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

scientific article published on 25 May 2015

Assembly algorithms for next-generation sequencing data

scientific article

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

article

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

scientific article published on 02 August 2019

Author Correction: A robust benchmark for detection of germline large deletions and insertions

scientific article published on 22 July 2020

Author Correction: Improved reference genome of the arboviral vector Aedes albopictus

correction of a scholarly article

Automated ensemble assembly and validation of microbial genomes

scientific article

Bambus 2: scaffolding metagenomes

scientific article

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

scientific article

Complete Closed Genome Sequences of Four Mannheimia varigena Isolates from Cattle with Shipping Fever

scientific article published on 13 February 2014

Complete Closed Genome Sequences of Mannheimia haemolytica Serotypes A1 and A6, Isolated from Cattle

scientific article published on 16 May 2013

Complete Closed Genome Sequences of Three Bibersteinia trehalosi Nasopharyngeal Isolates from Cattle with Shipping Fever

scientific article published on 13 February 2014

Complete Genome Sequence of the Quality Control Strain Staphylococcus aureus subsp. aureus ATCC 25923.

scientific article

Complete genomic and epigenetic maps of human centromeres

scientific article published in April 2022

Complete genomic and epigenetic maps of human centromeres

scientific article published on 13 July 2021

Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

scientific article published on 29 April 2021

Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle

scientific article published on 01 April 2020

Corrigendum: Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

scientific article published in October 2015

De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing.

scientific article published on 12 October 2017

De Novo assembly of the goldfish ( Carassius auratus ) genome and the evolution of genes after whole genome duplication

article

De novo assembly of haplotype-resolved genomes with trio binning

article

De novo assembly of the cattle reference genome with single-molecule sequencing

scientific article published on 01 March 2020

De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication.

scientific article published on 26 June 2019

De novo likelihood-based measures for comparing genome assemblies

scientific article

Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers

scientific article

Draft Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains, Isolated from the International Space Station.

scientific article published on 10 August 2017

Effect of sequence depth and length in long-read assembly of the maize inbred NC358

scientific article published on 08 May 2020

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

scientific article

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

scientific article published on 02 January 2020

Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

scientific article published on 28 April 2021

GAGE: A critical evaluation of genome assemblies and assembly algorithms

scientific article published on 6 January 2012

Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres

scientific article published on 17 April 2014

Genomic exploration of individual giant ocean viruses

scientific article published on 12 May 2017

Genomic insights into the Ixodes scapularis tick vector of Lyme disease

scientific article published on 9 February 2016

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

scientific article published on 10 October 2024

HLA*LA - HLA typing from linearly projected graph alignments

scientific article published on 01 November 2019

HLA*PRG:LA - HLA typing from linearly projected graph alignments

Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle

scientific article published on 29 April 2020

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

scientific article published on 14 August 2020

High-coverage sequencing and annotated assemblies of the budgerigar genome

scientific article

Highly-accurate long-read sequencing improves variant detection and assembly of a human genome: Supplementary Material

article

Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm

scientific article published on 27 January 2017

Hybrid error correction and de novo assembly of single-molecule sequencing reads

scientific article

Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control

Improved reference genome of Aedes aegypti informs arbovirus vector control

scientific article published in Nature

Improved reference genome of the arboviral vector Aedes albopictus

scientific article published on 26 August 2020

Increased mutation and gene conversion within human segmental duplications

scientific article published on 10 May 2023

Integrating Hi-C links with assembly graphs for chromosome-scale assembly

Integrating Hi-C links with assembly graphs for chromosome-scale assembly

scientific article published on 21 August 2019

Leveraging evolutionary relationships to improve Anopheles genome assemblies

Linking the Resistome to the Microbiome: A Culture-Free Method Links Plasmid, Virus, and Antimicrobial Resistance Genes to their Hosts in Complex Microbial Populations

scientific article published in December 2019

Mash Screen: High-throughput sequence containment estimation for genome discovery

scientific article published in March 2019

Mash Screen: high-throughput sequence containment estimation for genome discovery

scientific article published on 05 November 2019

Mash: fast genome and metagenome distance estimation using MinHash

scientific article

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

scientific article published on 14 September 2020

MetAMOS: a metagenomic assembly and analysis pipeline for AMOS.

scientific article published on 19 September 2011

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

scientific article

MetaMaps - Strain-level metagenomic assignment and compositional estimation for long reads

article

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes

scientific article

Molecular epidemiologic investigation of an anthrax outbreak among heroin users, Europe

scientific article

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

article

Nanopore sequencing and assembly of a human genome with ultra-long reads.

scientific article published on 29 January 2018

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

scientific article published on 04 May 2020

New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes

scientific article published on 19 December 2019

Next generation sequence assembly with AMOS.

scientific article

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

scientific article

Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes

scientific article published on 29 March 2016

Reducing assembly complexity of microbial genomes with single-molecule sequencing

scientific article

RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification

Reply to 'Errors in long-read assemblies can critically affect protein prediction'

scientific article published on 01 February 2019

SMRT® Sequencing Solutions for Large Genomes and Transcriptomes

scientific article published in May 2014

ScaffViz: visualizing metagenome assemblies.

scientific article published on 19 September 2011

Scaffolding of long read assemblies using long range contact information

scientific article

Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton

scientific article

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

scientific article published on 6 March 2017

Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps

scientific article published on 11 July 2019

Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential

scientific article published on 08 January 2020

Structure, function and diversity of the healthy human microbiome

scientific article

Telomere-to-telomere assembly of a complete human X chromosome

scientific article published on 14 July 2020

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes

preprint article published in December 2023

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes

scientific article

The bonobo genome compared with the chimpanzee and human genomes

scientific article

The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts

scientific article

The complete sequence and comparative analysis of ape sex chromosomes

scholarly article published in June 2024

The complete sequence of a human Y chromosome

The complete sequence of a human genome

scientific article published in April 2022

The complete sequence of a human genome

scientific article published on 27 May 2021

The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation

scientific article published on 09 February 2017

The genome of the zebra mussel, <i>Dreissena polymorpha</i>: a resource for comparative genomics, invasion genetics, and biocontrol

scientific article published on 13 December 2021

The structure, function and evolution of a complete human chromosome 8

scientific article published on 07 April 2021

The whale shark genome reveals patterns of vertebrate gene family evolution

scientific article published on 19 August 2021

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

scientific article

Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing

article

Weighted minimizer sampling improves long read mapping

scientific article published on 01 July 2020

Whole-Genome Sequences of 80 Environmental and Clinical Isolates of Burkholderia pseudomallei

scientific article

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