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List of works by Benedict Paten

A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0).

scientific article published on 30 October 2017

A draft human pangenome reference

scientific article published on 10 May 2023

A graph extension of the positional Burrows-Wheeler transform and its applications

scientific article

A unifying model of genome evolution under parsimony

scientific article

Accurate reconstruction of insertion-deletion histories by statistical phylogenetics

scientific article

Alignathon: a competitive assessment of whole-genome alignment methods

scientific article

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

scientific article

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

scientific article published in June 2007

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

BioHackathon 2015: Semantics of data for life sciences and reproducible research

scientific article published on 24 February 2020

Building a collaborative cloud platform to accelerate heart, lung, blood, and sleep research

scientific article published in 2023

Building a pan-genome reference for a population

scientific article published on 7 January 2015

Cactus Graphs for Genome Comparisons

scientific article (publication date: 2010)

Cactus graphs for genome comparisons

scientific article published in March 2011

Cactus: Algorithms for genome multiple sequence alignment

scientific article published on 10 June 2011

Canonical, stable, general mapping using context schemes ⬇️

scientific article published on 27 July 2015

Comparative Annotation Toolkit (CAT) - simultaneous clade and personal genome annotation

article published in 2017

Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation

Comparative assembly hubs: web-accessible browsers for comparative genomics

scientific article published on 18 August 2014

Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs ⬇️

DATA SHARING AND REPRODUCIBLE CLINICAL GENETIC TESTING: SUCCESSES AND CHALLENGES.

scientific article

Dense sampling of bird diversity increases power of comparative genomics

scientific article published on 11 November 2020

Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop

scientific article

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

scientific article

Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs

scientific article

Erratum to: The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

scientific article published on 13 December 2016

Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells.

scientific article published on 24 May 2018

Evolutionary constraint and innovation across hundreds of placental mammals

scientific article published on 28 April 2023

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

scientific article published on 07 December 2020

Genetic Site-Aware Three-Dimensional Layout Algorithm for Variation Graphs

scientific article published on 04 October 2023

Genome graphs and the evolution of genome inference

scientific article

Genome-wide nucleotide-level mammalian ancestor reconstruction

scientific article (publication date: November 2008)

HAL: a hierarchical format for storing and analyzing multiple genome alignments

scientific article

Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

scientific article published on 01 November 2021

High-resolution comparative analysis of great ape genomes

scientific article published in Science

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Improved data analysis for the MinION nanopore sequencer

scientific article

Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling

scientific article

Increased mutation and gene conversion within human segmental duplications

scientific article published on 10 May 2023

Insights into mammalian TE diversity through the curation of 248 genome assemblies ⬇️

Integrating gene annotation with orthology inference at scale ⬇️

scientific article published on 28 April 2023

Long-read sequence assembly of the gorilla genome

scientific article published on April 2016

Mapping DNA methylation with high-throughput nanopore sequencing

scientific article published on 20 February 2017

Meta-alignment with crumble and prune: partitioning very large alignment problems for performance and parallelization ⬇️

scientific article

Modelling haplotypes with respect to reference cohort variation graphs

scientific article published on July 2017

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

article

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

scientific article published on 04 May 2020

Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans

Progressive Cactus is a multiple-genome aligner for the thousand-genome era

scientific article published on 11 November 2020

Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era

scientific article published on 9 August 2019

Ragout-a reference-assisted assembly tool for bacterial genomes

scientific article

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

scientific article published on 21 March 2018

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs

scientific article

Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility

scientific article

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.

scientific article

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

scientific article published on 14 July 2020

The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows

scientific article

The Genome 10K Project: a way forward

scientific article

The Human Cell Atlas White Paper ⬇️

journal article from 'arXiv:1810.05192 [q-bio]' published in 2018

The Human Pangenome Project: a global resource to map genomic diversity

scientific article published in April 2022

The Matchmaker Exchange: a platform for rare disease gene discovery

scientific article

The NIH BD2K center for big data in translational genomics

scientific article

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

scientific article

The UCSC Genome Browser database: 2015 update

scientific article

The UCSC Genome Browser database: 2016 update

scientific article

The contribution of historical processes to contemporary extinction risk in placental mammals ⬇️

The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates

scientific article published on 2 December 2005

The functional and evolutionary impacts of human-specific deletions in conserved elements ⬇️

The genome of C57BL/6J "Eve", the mother of the laboratory mouse genome reference strain

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

scientific article

Three-dimensional genome rewiring in loci with human accelerated regions ⬇️

scientific article published on 28 April 2023

Toil enables reproducible, open source, big biomedical data analyses

scientific article

Toward a data infrastructure for the Plant Cell Atlas

scientific article published on 6 October 2022

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

scientific article

Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures

scientific article published on 11 November 2021

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

scientific article

Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation

scientific article published on 24 June 2007

Using Trawler_standalone to discover overrepresented motifs in DNA and RNA sequences derived from various experiments including chromatin immunoprecipitation

scientific article

Whole-Genome Alignment and Comparative Annotation

scientific article published on 31 October 2018

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