Lista de obras - Sergey Koren - Dominio Público Uruguay

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

artículo científico publicado en 2009

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

artículo científico publicado en 2018

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

artículo científico publicado en 2012

A robust benchmark for detection of germline large deletions and insertions

artículo científico publicado en 2020

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

artículo científico publicado en 2019

Aggressive assembly of pyrosequencing reads with mates

artículo científico publicado en 2008

An algorithm for automated closure during assembly

artículo científico publicado en 2010

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

artículo científico publicado en 2020

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

artículo científico publicado en 2018

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

artículo científico publicado en 2011

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

artículo científico publicado en 2013

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

artículo científico publicado en 2015

Assembly algorithms for next-generation sequencing data

artículo científico publicado en 2010

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

artículo científico publicado en 2020

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

artículo científico publicado en 2021

Automated ensemble assembly and validation of microbial genomes

artículo científico publicado en 2014

Bambus 2: scaffolding metagenomes

artículo científico publicado en 2011

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

artículo científico publicado en 2017

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

artículo científico publicado en 2013

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

artículo científico publicado en 2014

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

artículo científico publicado en 2014

Complete genomic and epigenetic maps of human centromeres

artículo científico publicado en 2022

Complete genomic and epigenetic maps of human centromeres

artículo científico publicado en 2021

Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

artículo científico publicado en 2021

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

artículo científico publicado en 2020

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

artículo científico publicado en 2015

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

artículo científico publicado en 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

artículo científico publicado en 2020

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

artículo científico publicado en 2019

De novo likelihood-based measures for comparing genome assemblies

artículo científico publicado en 2013

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

artículo científico publicado en 2016

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

artículo científico publicado en 2017

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

artículo científico publicado en 2020

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

artículo científico publicado en 2017

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

artículo científico publicado en 2020

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

artículo científico publicado en 2021

GAGE: A critical evaluation of genome assemblies and assembly algorithms

artículo científico publicado en 2012

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

artículo científico publicado en 2014

Genomic exploration of individual giant ocean viruses

artículo científico publicado en 2017

Genomic insights into the Ixodes scapularis tick vector of Lyme disease

artículo científico publicado en 2016

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

artículo científico publicado en 2024

HLA*LA - HLA typing from linearly projected graph alignments

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2014

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

artículo científico publicado en 2017

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

artículo científico publicado en 2012

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

artículo científico publicado en 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

artículo científico publicado en 2019

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

artículo científico publicado en 2019

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

artículo científico publicado en 2019

Mash: fast genome and metagenome distance estimation using MinHash

artículo científico publicado en 2016

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.

artículo científico publicado en 2011

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

artículo científico publicado en 2013

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

artículo científico publicado en 2017

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

artículo científico publicado en 2012

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.

artículo científico publicado en 2018

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

artículo científico publicado en 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.

artículo científico publicado en 2011

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

artículo científico publicado en 2014

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

artículo científico publicado en 2016

Reducing assembly complexity of microbial genomes with single-molecule sequencing

artículo científico publicado en 2013

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'

artículo científico publicado en 2019

SMRT® Sequencing Solutions for Large Genomes and Transcriptomes

artículo científico publicado en 2014

ScaffViz: visualizing metagenome assemblies.

artículo científico publicado en 2011

Scaffolding of long read assemblies using long range contact information

artículo científico publicado en 2017

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

artículo científico publicado en 2015

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

artículo científico publicado en 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

artículo científico publicado en 2012

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

artículo científico publicado en 2020

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes

artículo científico publicado en 2023

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

artículo científico publicado en 2014

The bonobo genome compared with the chimpanzee and human genomes

artículo científico publicado en 2012

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

artículo científico publicado en 2016

The complete sequence and comparative analysis of ape sex chromosomes

artículo científico publicado en 2024

The complete sequence of a human Y chromosome

The complete sequence of a human genome

artículo científico publicado en 2022

The complete sequence of a human genome

artículo científico publicado en 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

artículo científico publicado en 2021

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

artículo científico publicado en 2021

The whale shark genome reveals patterns of vertebrate gene family evolution

artículo científico publicado en 2021

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

artículo científico publicado en 2021

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

article

Weighted minimizer sampling improves long read mapping

artículo científico publicado en 2020

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

artículo científico publicado en 2015

Lista de obras de 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

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

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

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

A draft human pangenome reference

A fast adaptive algorithm for computing whole-genome homology maps

A framework for human microbiome research

A robust benchmark for detection of germline large deletions and insertions

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

Aggressive assembly of pyrosequencing reads with mates

An algorithm for automated closure during assembly

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

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

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

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

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

Assembly algorithms for next-generation sequencing data

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

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

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

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

Automated ensemble assembly and validation of microbial genomes

Bambus 2: scaffolding metagenomes

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

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

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

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

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

Complete genomic and epigenetic maps of human centromeres

Complete genomic and epigenetic maps of human centromeres

Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

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

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

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

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

De novo assembly of haplotype-resolved genomes with trio binning

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

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

De novo likelihood-based measures for comparing genome assemblies

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

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

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

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

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

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

GAGE: A critical evaluation of genome assemblies and assembly algorithms

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

Genomic exploration of individual giant ocean viruses

Genomic insights into the Ixodes scapularis tick vector of Lyme disease

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

HLA*LA - HLA typing from linearly projected graph alignments

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

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

High-coverage sequencing and annotated assemblies of the budgerigar genome

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

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

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

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

Improved reference genome of Aedes aegypti informs arbovirus vector control

Improved reference genome of the arboviral vector Aedes albopictus

Increased mutation and gene conversion within human segmental duplications

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

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

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

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

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

Mash: fast genome and metagenome distance estimation using MinHash

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

MetAMOS: a metagenomic assembly and analysis pipeline for AMOS.

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

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

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

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

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

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

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