Sergey Koren | Academic Influence

Sergey Koren's AcademicInfluence.com Rankings

Sergey Koren

Biology

#13804

World Rank

#17385

Historical Rank

Bioinformatics

#177

World Rank

#179

Historical Rank

Computational Biology

#328

World Rank

#329

Historical Rank

biology Degrees

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Biology

Sergey Koren's Degrees

PhD Bioinformatics University of California, Santa Cruz
Masters Computer Science University of California, Santa Cruz
Bachelors Computer Science University of California, Santa Cruz

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Why Is Sergey Koren Influential?

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According to Wikipedia, Sergey Koren is an American bioinformatician who is an associate investigator in the genome informatics section at the National Human Genome Research Institute. After completing his M.S., Koren joined the J. Craig Venter Institute as a bioinformatics engineer under the supervision of Granger Sutton. During his three years at JCVI, he contributed to the development of the Celera Assembler, which has been used to assemble both the Drosophila melanogaster and human genomes. In parallel, Koren worked under the supervision Mihai Pop at the University of Maryland, College Park, where he developed several tools for metagenome assembly and analysis.

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Sergey Koren's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

Structure, Function and Diversity of the Healthy Human Microbiome (2012) (8630)
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. (2017) (4153)
A framework for human microbiome research (2012) (2113)
Mash: fast genome and metagenome distance estimation using MinHash (2015) (1626)
Nanopore sequencing and assembly of a human genome with ultra-long reads (2017) (1276)
Assembly algorithms for next-generation sequencing data. (2010) (1108)
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes (2014) (1103)
Hybrid error correction and de novo assembly of single-molecule sequencing reads (2012) (947)
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing (2014) (828)
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome (2019) (706)
GAGE: A critical evaluation of genome assemblies and assembly algorithms. (2012) (702)
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species (2013) (702)
The complete sequence of a human genome (2021) (622)
Aggressive assembly of pyrosequencing reads with mates (2008) (562)
Towards complete and error-free genome assemblies of all vertebrate species (2020) (557)
Assemblathon 1: a competitive assessment of de novo short read assembly methods. (2011) (542)
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. (2017) (541)
The bonobo genome compared with the chimpanzee and human genomes (2012) (455)
Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome (2017) (450)
Telomere-to-telomere assembly of a complete human X chromosome (2019) (450)
Genomic insights into the Ixodes scapularis tick vector of Lyme disease (2016) (391)
Reducing assembly complexity of microbial genomes with single-molecule sequencing (2013) (369)
One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. (2015) (367)
Integrating Hi-C links with assembly graphs for chromosome-scale assembly (2018) (342)
Improved reference genome of Aedes aegypti informs arbovirus vector control (2018) (316)
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads (2020) (284)
Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the mega-reads algorithm (2016) (283)
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies (2020) (276)
De novo assembly of the cattle reference genome with single-molecule sequencing (2020) (274)
De novo assembly of haplotype-resolved genomes with trio binning (2018) (262)
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes (2020) (241)
The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts (2016) (227)
Next Generation Sequence Assembly with AMOS (2011) (212)
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline (2013) (197)
Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton (2015) (180)
A robust benchmark for detection of germline large deletions and insertions (2020) (171)
An improved pig reference genome sequence to enable pig genetics and genomics research (2019) (152)
The structure, function and evolution of a complete human chromosome 8 (2020) (146)
Bambus 2: scaffolding metagenomes (2011) (146)
De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing[CC-BY] (2017) (145)
Mash Screen: high-throughput sequence containment estimation for genome discovery (2019) (130)
Scaffolding of long read assemblies using long range contact information (2016) (129)
De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication (2019) (100)
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes (2019) (94)
Complete genomic and epigenetic maps of human centromeres (2021) (90)
High-coverage sequencing and annotated assemblies of the budgerigar genome (2014) (87)
RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification (2018) (85)
Weighted minimizer sampling improves long read mapping (2020) (83)
A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases (2017) (81)
Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes (2016) (80)
A fast adaptive algorithm for computing whole-genome homology maps (2018) (79)
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps (2019) (75)
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation (2016) (72)
A complete reference genome improves analysis of human genetic variation (2021) (68)
Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres (2014) (65)
Automated ensemble assembly and validation of microbial genomes (2014) (63)
HLA*LA—HLA typing from linearly projected graph alignments (2019) (61)
Complete Genome Sequence of the Quality Control Strain Staphylococcus aureus subsp. aureus ATCC 25923 (2014) (58)
Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation (2018) (57)
Segmental duplications and their variation in a complete human genome (2021) (57)
Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle (2020) (56)
Amycomicin is a potent and specific antibiotic discovered with a targeted interaction screen (2018) (55)
A robust benchmark for germline structural variant detection (2019) (54)
Improved reference genome of the arboviral vector Aedes albopictus (2020) (53)
Highly-accurate long-read sequencing improves variant detection and assembly of a human genome (2019) (52)
Epigenetic Patterns in a Complete Human Genome (2021) (52)
De novo likelihood-based measures for comparing genome assemblies (2013) (52)
De Novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole genome duplication (2018) (47)
Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing (2018) (46)
A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads (2009) (46)
Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation (2018) (43)
Efficient de novo assembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit (2019) (43)
Complete vertebrate mitogenomes reveal widespread repeats and gene duplications (2021) (41)
Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C (2021) (39)
Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies (2018) (37)
De novo assembly of a new Solanum pennellii accession using nanopore sequencing (2020) (37)
Semi-automated assembly of high-quality diploid human reference genomes (2022) (37)
Effect of sequence depth and length in long-read assembly of the maize inbred NC358 (2019) (37)
Extended haplotype phasing of de novo genome assemblies with FALCON-Phase (2019) (36)
A chromosome-scale assembly of the major African malaria vector Anopheles funestus (2018) (36)
A draft genome sequence for the Ixodes scapularis cell line, ISE6 (2018) (36)
Genomic exploration of individual giant ocean viruses (2017) (35)
The complete sequence of a human Y chromosome (2022) (35)
Merqury: reference-free quality and phasing assessment for genome assemblies (2020) (34)
Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential (2019) (33)
Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle (2020) (33)
Modernizing the Bovine Reference Genome Assembly (2018) (31)
Whole-Genome Sequences of 80 Environmental and Clinical Isolates of Burkholderia pseudomallei (2015) (29)
Long-read mapping to repetitive reference sequences using Winnowmap2 (2022) (28)
Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control (2017) (28)
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies (2021) (27)
De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads (2018) (26)
Complete Closed Genome Sequences of Mannheimia haemolytica Serotypes A1 and A6, Isolated from Cattle (2013) (24)
A long read mapping method for highly repetitive reference sequences (2020) (24)
The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation (2016) (23)
Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes (2016) (23)
New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes (2019) (22)
Evolutionary and biomedical insights from a marmoset diploid genome assembly (2021) (22)
Reply to ‘Errors in long-read assemblies can critically affect protein prediction’ (2019) (22)
Complete assembly of parental haplotypes with trio binning (2018) (20)
Verkko: telomere-to-telomere assembly of diploid chromosomes (2022) (19)
Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential (2020) (19)
Corrigendum: Assembling large genomes with single-molecule sequencing and locality-sensitive hashing (2015) (19)
MetaCompass: Reference-guided Assembly of Metagenomes (2017) (17)
The Genome of the Zebra Mussel, Dreissena polymorpha: A Resource for Invasive Species Research (2019) (17)
Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers (2016) (16)
An algorithm for automated closure during assembly (2010) (14)
MetAMOS: a metagenomic assembly and analysis pipeline for AMOS (2011) (14)
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome (2019) (13)
Merfin: improved variant filtering and polishing via k-mer validation (2021) (12)
The whale shark genome reveals patterns of vertebrate gene family evolution (2019) (12)
A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.) (2020) (11)
Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation (2022) (11)
Complete Closed Genome Sequences of Three Bibersteinia trehalosi Nasopharyngeal Isolates from Cattle with Shipping Fever (2014) (11)
Rapid Core-Genome Alignment and Visualization for Thousands of Intraspecific Microbial Genomes (2014) (10)
Draft Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains, Isolated from the International Space Station (2017) (10)
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes (2020) (9)
MetaMaps – Strain-level metagenomic assignment and compositional estimation for long reads (2018) (9)
RefSeq database growth influences the accuracy of k-mer-based species identification (2018) (9)
Telomere-to-telomere assembly of diploid chromosomes with Verkko. (2023) (8)
Complete Closed Genome Sequences of Four Mannheimia varigena Isolates from Cattle with Shipping Fever (2014) (8)
Chromosome-length haplotigs for yak and cattle from trio binning assembly of an F1 hybrid (2019) (8)
MetAMOS: a metagenomic assembly and analysis pipeline for AMOS (2011) (8)
Complete vertebrate mitogenomes reveal widespread gene duplications and repeats (2020) (7)
Improved reference genome of Aedes aegypti informs arbovirus vector control (2018) (7)
The genome of the zebra mussel, Dreissena polymorpha: a resource for comparative genomics, invasion genetics, and biocontrol (2021) (6)
HLA*PRG:LA – HLA typing from linearly projected graph alignments (2018) (5)
Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation (2019) (5)
The Genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success (2022) (5)
Approaches taken, progress made, and enhanced utility of long read-based goat, swine, cattle and sheep reference genomes (2016) (4)
Title: A complete human reference genome improves variant calling for population and clinical genomics (2021) (4)
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly (2016) (4)
Recombination between heterologous human acrocentric chromosomes (2023) (3)
Leveraging evolutionary relationships to improve Anopheles genome assemblies (2018) (3)
Improved sequence mapping using a complete reference genome and lift-over (2022) (3)
Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle (2020) (3)
SMRT® Sequencing Solutions for Large Genomes and Transcriptomes (2014) (3)
A robust benchmark for detection of germline large deletions and insertions (2020) (2)
De novo likelihood-based measures for comparing metagenomic assemblies (2013) (2)
How to Compare and Cluster Every Known Genome in about an Hour (2016) (2)
Complete vertebrate mitogenomes reveal widespread repeats and gene duplications (2021) (2)
ScaffViz: visualizing metagenome assemblies (2011) (2)
A family of unusual immunoglobulin superfamily genes in an invertebrate histocompatibility complex (2022) (2)
Genome Assembly: Novel Applications by Harnessing Emerging Sequencing Technologies and Graph Algorithms (2012) (1)
Reducing assembly complexity of microbial genomes with single-molecule sequencing (2013) (1)
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes (2014) (1)
Amycomicin: a potent and specific antibiotic discovered with a targeted interaction screen (2018) (1)
nsemble assembly and validation of microbial genomes (2014) (1)
De novo likelihood-based measures for comparing genome assemblies (2013) (1)
Reducing Assembly Complexity with Single-Molecule Sequencing (2014) (1)
From Sequencing to Chromosomes: New de novo Assembly and Scaffolding Methods Improve the Goat Reference Genome (2016) (1)
Author Correction: A robust benchmark for detection of germline large deletions and insertions (2020) (1)
Improved reference genome of the arboviral vector Aedes albopictus (2020) (1)
The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation (2017) (1)
Analysis of the Aedes albopictus C6/36 genome provides insight into cell line adaptations to in vitro viral propagation (2017) (1)
Accelerating error correction and assembly of single-molecule sequencing reads (2013) (1)
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies (2020) (0)
Chromosome scale de novo assembly of genomes using chromatin interaction data (2017) (0)
- 1-Rapid CoreG enome A lignment and V isualization f or T housands of Intraspecific M icrobial Genomes (2014) (0)
New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes (2019) (0)
Expansion of a Framework for a Data-Intensive Wide-Area Application to the Java Language (2002) (0)
Mash: fast genome and metagenome distance estimation using MinHash (2016) (0)
A robust benchmark for germline large deletion and insertion detection (0)
De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads (2018) (0)
de novo Metagenomic Assembly (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time) (2011) (0)
Metagenomic Assembly using Graph Algorithm and Applications (2009) (0)
Phased nanopore assembly with Shasta and modular graph phasing with GFAse (2023) (0)
Metagenomic assembly through the lens of validation: a review of recent advances in assessing and improving the quality of genes and genomes assembled from metagenomes. (2017) (0)
Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions (2023) (0)
Genome and Genetic Engineering of the House Cricket (Acheta domesticus): A Resource for Sustainable Agriculture (2023) (0)
Automated ensemble assembly and validation of microbial genomes (2014) (0)
A framework for human microbiome research A framework for human microbiome research (2020) (0)
Telomere-to-telomere assembly of a complete human X chromosome (2020) (0)
Author Correction: Improved reference genome of the arboviral vector Aedes albopictus (2021) (0)
Effect of sequence depth and length in long-read assembly of the maize inbred NC358 (2020) (0)
Linking the Resistome to the Microbiome: A Culture-Free Method Links Plasmid, Virus, and Antimicrobial Resistance Genes to their Hosts in Complex Microbial Populations. (2019) (0)
Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies (2020) (0)
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline (2013) (0)
Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome (2017) (0)
Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains , Isolated from the International Space Station Venkateswaran (2017) (0)
Mash Screen: high-throughput sequence containment estimation for genome discovery (2019) (0)
Genome and Genetic Engineering of the House Cricket (Acheta domesticus): Applications for Sustainable Agriculture (2022) (0)
Scaffolding of long read assemblies using long range contact information (2017) (0)
Celera Assembler and Automated Finishing (2009) (0)
Chromosome-Length Haplotigs for Cattle and Yak from Trio-Binning Assembly of an F1 Hybrid (2019) (0)
A draft genome sequence for the Ixodes scapularis cell line, ISE6 [version 1; peer review: 2 approved] (2021) (0)
RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification (2018) (0)
Correction to: The genome of the zebra mussel, Dreissena polymorpha: a resource for comparative genomics, invasion genetics, and biocontrol (2022) (0)
ScaffViz: visualizing metagenome assemblies (2011) (0)
New Insights into Mammalian Sex Chromosome Structure and Evolution from High-quality Bovine X and Y Chromosome Sequences (2019) (0)
Efficient Assembly of Large Genomes Using Single-Molecule Sequencing and Locality Sensitive Hashing (2015) (0)
Reply to ‘Errors in long-read assemblies can critically affect protein prediction’ (2019) (0)
De novo long-read assembly of a complex animal genome (2017) (0)
A Tale of Three Beetles: Lessons Learned from Sequencing and Assembling the Genome of Stored Product Insects (2018) (0)
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps (2019) (0)
Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation (2019) (0)

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Other Resources About Sergey Koren

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What Schools Are Affiliated With Sergey Koren?

Sergey Koren is affiliated with the following schools:

University of California, Santa Cruz