List of works by Adam Phillippy

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 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 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

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

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

Automated ensemble assembly and validation of microbial genomes

scientific article

Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation

scientific article

Balancing openness with Indigenous data sovereignty: An opportunity to leave no one behind in the journey to sequence all of life

scientific article published on 18 January 2022

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

scientific article

Comparative genome assembly.

scientific article published in September 2004

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 vertebrate mitogenomes reveal widespread repeats and gene duplications

scientific article published on 29 April 2021

Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis

scientific article published on 28 November 2011

Comprehensive DNA signature discovery and validation

scientific article

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

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

Efficient oligonucleotide probe selection for pan-genomic tiling arrays

scientific article

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

scientific article

Evolution of genes and genomes on the Drosophila phylogeny

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

Fast algorithms for large-scale genome alignment and comparison ⬇️

scientific article

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

scientific article published in April 2022

GAGE: A critical evaluation of genome assemblies and assembly algorithms

scientific article published on 6 January 2012

Genome Sequence of the Attenuated Carbosap Vaccine Strain of Bacillus anthracis

scientific article published on 15 January 2013

Genome Sequence of the PCE-Dechlorinating Bacterium Dehalococcoides ethenogenes

scientific article

Genome assembly forensics: finding the elusive mis-assembly

scientific article

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.

scientific article

Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs

scientific article published on 04 August 2020

Genomic comparison of multi-drug resistant invasive and colonizing Acinetobacter baumannii isolated from diverse human body sites reveals genomic plasticity

scientific article

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

Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies

scientific article published on 23 December 2011

Hawkeye: an interactive visual analytics tool for genome assemblies

scientific article published on January 2007

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

scientific article published on 14 August 2020

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

scientific article published in Nature Communications

High-coverage sequencing and annotated assemblies of the budgerigar genome

scientific article

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

scientific article

Identification and Genomic Analysis of a Novel Group C Orthobunyavirus Isolated from a Mosquito Captured near Iquitos, Peru

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

Increased mutation and gene conversion within human segmental duplications

scientific article published on 10 May 2023

Insignia: a DNA signature search web server for diagnostic assay development

scientific article published on 5 May 2009

Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray

scientific article

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

Interactive metagenomic visualization in a Web browser

scientific article

Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone

scientific article (publication date: 27 December 2012)

Leveraging evolutionary relationships to improve Anopheles genome assemblies

Long-read, whole-genome shotgun sequence data for five model organisms

scientific article

MUMmer4: A fast and versatile genome alignment system

scientific article

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

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

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.

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 advances in sequence assembly

scientific article

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

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

scientific article

Platypus and echidna genomes reveal mammalian biology and evolution

scientific article published on 06 January 2021

Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification

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

Reference genome and demographic history of the most endangered marine mammal, the vaquita

scientific article published on 22 October 2020

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

scientific article published on 01 February 2019

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

scientific article published on 6 March 2017

Standards recommendations for the Earth BioGenome Project

scientific article published on 18 January 2022

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

Strategic vision for improving human health at The Forefront of Genomics

scientific article published on 28 October 2020

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

scientific article published on 14 July 2020

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

scientific article

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

scientific article

The complete sequence of a human Y chromosome

The complete sequence of a human genome

scientific article published in April 2022

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 rise of a digital immune system

scientific article

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

scientific article published on 07 April 2021

Transcriptomic responses of Salmonella enterica serovars Enteritidis and Typhimurium to chlorine-based oxidative stress

scientific article

Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp.

scientific article

Using MUMmer to identify similar regions in large sequence sets.

scientific article published in February 2003

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

article

Versatile and open software for comparing large genomes

scientific article

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