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

Nature Communications
2020-12 | Journal article
DOI: 10.1038/s41467-020-16037-7
Part of ISSN: 2041-1723
Source: Self-asserted source
Sergey Koren
grade
Preferred source (of 2)‎

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

BMC Biology
2020-12 | Journal article
DOI: 10.1186/s12915-019-0728-3
Part of ISSN: 1741-7007
Source: Self-asserted source
Sergey Koren

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

Nature Communications
2020-12 | Journal article
DOI: 10.1038/s41467-020-15848-y
Part of ISSN: 2041-1723
Source: Self-asserted source
Sergey Koren

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

Genome Medicine
2020-12 | Journal article
DOI: 10.1186/s13073-019-0708-9
Part of ISSN: 1756-994X
Source: Self-asserted source
Sergey Koren

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

Genome biology
2020-09-14 | Journal article
DOI: 10.1186/s13059-020-02134-9
PMID: 32928274
PMC: PMC7488777
Source: Self-asserted source
Sergey Koren

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

Nature
2020-09-03 | Journal article
DOI: 10.1038/s41586-020-2547-7
Part of ISSN: 0028-0836
Part of ISSN: 1476-4687
Source: Self-asserted source
Sergey Koren

Improved reference genome of the arboviral vector Aedes albopictus.

Genome biology
2020-08-26 | Journal article
DOI: 10.1186/s13059-020-02141-w
PMID: 32847630
PMC: PMC7448346
Source: Self-asserted source
Sergey Koren
grade
Preferred source (of 2)‎

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

Genome research
2020-08-14 | Journal article
DOI: 10.1101/gr.263566.120
PMID: 32801147
PMC: PMC7545148
Source: Self-asserted source
Sergey Koren

Weighted minimizer sampling improves long read mapping

Bioinformatics
2020-07-01 | Journal article
DOI: 10.1093/bioinformatics/btaa435
Part of ISSN: 1367-4803
Part of ISSN: 1460-2059
Source: Self-asserted source
Sergey Koren

A robust benchmark for detection of germline large deletions and insertions.

Nature biotechnology
2020-06-15 | Journal article
DOI: 10.1038/s41587-020-0538-8
PMID: 32541955
Source: Self-asserted source
Sergey Koren

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

GigaScience
2020-06-01 | Journal article
DOI: 10.1093/gigascience/giaa051
PMID: 32543654
PMC: PMC7448572
Source: Self-asserted source
Sergey Koren

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

Nature Biotechnology
2020-05-04 | Journal article
DOI: 10.1038/s41587-020-0503-6
Part of ISSN: 1087-0156
Part of ISSN: 1546-1696
Source: Self-asserted source
Sergey Koren

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

GigaScience
2020-04-01 | Journal article
DOI: 10.1093/gigascience/giaa029
Part of ISSN: 2047-217X
Source: Self-asserted source
Sergey Koren
grade
Preferred source (of 3)‎

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

GigaScience
2020-03-01 | Journal article
DOI: 10.1093/gigascience/giaa021
Part of ISSN: 2047-217X
Source: Self-asserted source
Sergey Koren

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

Genome Biology
2019-12 | Journal article
DOI: 10.1186/s13059-019-1760-x
Part of ISSN: 1474-760X
Source: Self-asserted source
Sergey Koren
grade
Preferred source (of 2)‎

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

Genome Biology
2019-12 | Journal article
DOI: 10.1186/s13059-019-1841-x
Part of ISSN: 1474-760X
Source: Self-asserted source
Sergey Koren

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

BMC Genomics
2019-12 | Journal article
DOI: 10.1186/s12864-019-6364-z
Part of ISSN: 1471-2164
Source: Self-asserted source
Sergey Koren

HLA*LA—HLA typing from linearly projected graph alignments

Bioinformatics
2019-11-01 | Journal article
DOI: 10.1093/bioinformatics/btz235
Part of ISSN: 1367-4803
Part of ISSN: 1460-2059
Source: Self-asserted source
Sergey Koren

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

Nature Biotechnology
2019-10 | Journal article
DOI: 10.1038/s41587-019-0217-9
Part of ISSN: 1087-0156
Part of ISSN: 1546-1696
Source: Self-asserted source
Sergey Koren

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

PLOS Computational Biology
2019-08-21 | Journal article
DOI: 10.1371/journal.pcbi.1007273
Part of ISSN: 1553-7358
Source: Self-asserted source
Sergey Koren

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

Briefings in Bioinformatics
2019-07-19 | Journal article
DOI: 10.1093/bib/bbx098
Part of ISSN: 1467-5463
Part of ISSN: 1477-4054
Source: Self-asserted source
Sergey Koren
grade
Preferred source (of 2)‎

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

Nature communications
2019-07-11 | Journal article
DOI: 10.1038/s41467-019-10934-2
PMID: 31296857
PMC: PMC6624308
Source: Self-asserted source
Sergey Koren

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

Science Advances
2019-06 | Journal article
DOI: 10.1126/sciadv.aav0547
Part of ISSN: 2375-2548
Source: Self-asserted source
Sergey Koren

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

GigaScience
2019-06-01 | Journal article
DOI: 10.1093/gigascience/giz063
Part of ISSN: 2047-217X
Source: Self-asserted source
Sergey Koren

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

Nature Biotechnology
2019-02 | Journal article
DOI: 10.1038/s41587-018-0005-y
Part of ISSN: 1087-0156
Part of ISSN: 1546-1696
Source: Self-asserted source
Sergey Koren

De novo assembly of haplotype-resolved genomes with trio binning

Nature Biotechnology
2018-12 | Journal article
DOI: 10.1038/nbt.4277
Part of ISSN: 1087-0156
Part of ISSN: 1546-1696
Source: Self-asserted source
Sergey Koren

De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads

BMC Biology
2018-12 | Journal article
DOI: 10.1186/s12915-017-0473-4
Part of ISSN: 1741-7007
Source: Self-asserted source
Sergey Koren
grade
Preferred source (of 3)‎

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

Genome Biology
2018-12 | Journal article
DOI: 10.1186/s13059-018-1554-6
Part of ISSN: 1474-760X
Source: Self-asserted source
Sergey Koren

Improved reference genome of Aedes aegypti informs arbovirus vector control

Nature
2018-11 | Journal article
DOI: 10.1038/s41586-018-0692-z
Part of ISSN: 0028-0836
Part of ISSN: 1476-4687
Source: Self-asserted source
Sergey Koren

Amycomicin is a potent and specific antibiotic discovered with a targeted interaction screen.

Proceedings of the National Academy of Sciences of the United States of America
2018-09-18 | Journal article
DOI: 10.1073/pnas.1807613115
PMID: 30228116
PMC: PMC6176635
Source: Self-asserted source
Sergey Koren

A fast adaptive algorithm for computing whole-genome homology maps

Bioinformatics
2018-09-01 | Journal article
DOI: 10.1093/bioinformatics/bty597
Part of ISSN: 1367-4803
Part of ISSN: 1460-2059
Source: Self-asserted source
Sergey Koren

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

Nucleic Acids Research
2018-07-27 | Journal article
DOI: 10.1093/nar/gky442
Part of ISSN: 0305-1048
Part of ISSN: 1362-4962
Source: Self-asserted source
Sergey Koren
grade
Preferred source (of 2)‎

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

Nature Biotechnology
2018-04 | Journal article
DOI: 10.1038/nbt.4060
Part of ISSN: 1087-0156
Part of ISSN: 1546-1696
Source: Self-asserted source
Sergey Koren

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

F1000Research
2018-03-08 | Journal article
DOI: 10.12688/f1000research.13635.1
PMID: 29707202
PMC: PMC5883391
Source: Self-asserted source
Sergey Koren

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

GigaScience
2018-03-01 | Journal article
DOI: 10.1093/gigascience/gix135
Part of ISSN: 2047-217X
Source: Self-asserted source
Sergey Koren

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

The Plant Cell
2017-10 | Journal article
DOI: 10.1105/tpc.17.00521
Part of ISSN: 1040-4651
Part of ISSN: 1532-298X
Source: Self-asserted source
Sergey Koren
grade
Preferred source (of 2)‎

Genomic exploration of individual giant ocean viruses.

The ISME journal
2017-08 | Journal article
DOI: 10.1038/ismej.2017.61
PMID: 28498373
Source: Self-asserted source
Sergey Koren via Europe PubMed Central

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

Genome announcements
2017-08-10 | Journal article
DOI: 10.1128/genomea.00680-17
PMID: 28798168
PMC: PMC5552977
Source: Self-asserted source
Sergey Koren
grade
Preferred source (of 2)‎

Scaffolding of long read assemblies using long range contact information.

BMC genomics
2017-07 | Journal article
DOI: 10.1186/s12864-017-3879-z
PMID: 28701198
PMC: PMC5508778
Source: Self-asserted source
Sergey Koren via Europe PubMed Central

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

Genome research
2017-05 | Journal article
DOI: 10.1101/gr.215087.116
PMID: 28298431
PMC: PMC5411767
Source: Self-asserted source
Sergey Koren via Europe PubMed Central

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

Nature genetics
2017-04 | Journal article
DOI: 10.1038/ng.3802
PMID: 28263316
Source: Self-asserted source
Sergey Koren via Europe PubMed Central

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

Immunogenetics
2017-04 | Journal article
DOI: 10.1007/s00251-017-0973-y
PMID: 28180967
PMC: PMC5350243
Source: Self-asserted source
Sergey Koren via Europe PubMed Central

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

Genome research
2017-04-10 | Journal article
DOI: 10.1101/gr.213611.116
PMID: 28396521
PMC: PMC5411779
Source: Self-asserted source
Sergey Koren
grade
Preferred source (of 2)‎

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

Genome research
2017-01-27 | Journal article
DOI: 10.1101/gr.213405.116
PMID: 28130360
PMC: PMC5411773
Source: Self-asserted source
Sergey Koren
grade
Preferred source (of 2)‎

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

PloS one
2016-09-09 | Journal article
DOI: 10.1371/journal.pone.0160574
PMID: 27611571
PMC: PMC5017753
Source: Self-asserted source
Sergey Koren
grade
Preferred source (of 2)‎

Mash: fast genome and metagenome distance estimation using MinHash.

Genome biology
2016-06 | Journal article
DOI: 10.1186/s13059-016-0997-x
PMID: 27323842
PMC: PMC4915045
Source: Self-asserted source
Sergey Koren via Europe PubMed Central

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

Nature communications
2016-06-02 | Journal article
DOI: 10.1038/ncomms11757
PMID: 27249958
PMC: PMC4895719
Source: Self-asserted source
Sergey Koren
grade
Preferred source (of 2)‎

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

Proceedings of the National Academy of Sciences of the United States of America
2016-04 | Journal article
DOI: 10.1073/pnas.1525164113
PMID: 27035980
PMC: PMC4839409
Source: Self-asserted source
Sergey Koren via Europe PubMed Central

Genomic insights into the Ixodes scapularis tick vector of Lyme disease.

Nature Communications
2016-02 | Journal article
DOI: 10.1038/ncomms10507
PMID: 26856261
PMC: PMC4748124
Source: Self-asserted source
Sergey Koren via Europe PubMed Central

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

The ISME Journal
2015-11 | Journal article
DOI: 10.1038/ismej.2015.48
PMID: 25848873
PMC: PMC4611503
Source: Self-asserted source
Sergey Koren via Europe PubMed Central
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