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D-Index & Metrics

Biology and Biochemistry

D-Index
87
Citations
44139
World Ranking
2769
National Ranking
1429

Overview

Benedict Paten is affiliated with the University of California, Santa Cruz in the United States. Their research contributions span multiple areas within biochemistry, genetics, and molecular biology, with a significant focus on genomics and phylogenetic studies. The body of work encompasses diverse topics including chromosomal and genetic variations, cancer genomics and diagnostics, RNA modifications related to cancer, as well as mechanisms of RNA and protein synthesis.

The scientist has published extensively, with notable papers including:

  • "The complete sequence of a human genome," 2022, published in Science
  • "GENCODE 2021," 2020, published in Nucleic Acids Research
  • "Telomere-to-telomere assembly of a complete human X chromosome," 2020, published in Nature
  • "Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes," 2020, published in Nature Biotechnology
  • "Progressive Cactus is a multiple-genome aligner for the thousand-genome era," 2020, published in Nature

Benedict Paten frequently collaborates with several coauthors, including:

  • Glenn Hickey
  • Evan E. Eichler
  • Mark Diekhans
  • Miten Jain
  • Kishwar Shafin

The most common publication venues for their research include:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Science
  • Zenodo (CERN European Organization for Nuclear Research)
  • Nature
  • Genome Research

Their main fields of study are focused on Biochemistry, Genetics and Molecular Biology.

Subfields within these areas include:

  • Molecular Biology
  • Genetics
  • Plant Science
  • Cancer Research
  • Artificial Intelligence

Key topics in their research portfolio are:

  • Genomics and Phylogenetic Studies
  • Chromosomal and Genetic Variations
  • Genomic variations and chromosomal abnormalities
  • Cancer Genomics and Diagnostics
  • RNA modifications and cancer
  • RNA and protein synthesis mechanisms
  • Genomics and Rare Diseases

Best Publications

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

    Ewan Birney;John A. Stamatoyannopoulos;Anindya Dutta;Roderic Guigó

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

    Arang Rhie;Shane A. McCarthy;Shane A. McCarthy;Olivier Fedrigo;Joana Damas

  • GENCODE reference annotation for the human and mouse genomes.

    Adam Frankish;Mark Diekhans;Anne-Maud Ferreira;Rory Baldwin Johnson

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

    Miten Jain;Sergey Koren;Karen H Miga;Josh Quick

  • A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

    Richard M. Myers;John Stamatoyannopoulos;Michael Snyder;Ian Dunham

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

    Miten Jain;Hugh E. Olsen;Benedict Paten;Mark Akeson

  • Toil enables reproducible, open source, big biomedical data analyses

    John Vivian;Arjun Arkal Rao;Frank Austin Nothaft;Christopher Ketchum

  • Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics.

    Alvaro N. Barbeira;Scott P. Dickinson;Rodrigo Bonazzola;Jiamao Zheng

  • The UCSC Genome Browser database: 2015 update

    Kate R. Rosenbloom;Joel Armstrong;Galt P. Barber;Jonathan Casper

  • Gencode 2021

    A. Frankish;M. Diekhans;I. Jungreis;J. Lagarde

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

    Keith R. Bradnam;Joseph N. Fass;Anton Alexandrov;Paul Baranay

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

    Karen H. Miga;Sergey Koren;Arang Rhie;Mitchell R. Vollger

  • Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

    Alexander Stark;Michael F Lin;Pouya Kheradpour;Jakob Skou Pedersen;Jakob Skou Pedersen

  • Improved data analysis for the MinION nanopore sequencer

    Miten Jain;Ian T Fiddes;Karen H Miga;Hugh E Olsen

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

    Keith R. Bradnam;Joseph N. Fass;Anton Alexandrov;Paul Baranay

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

    Dent Earl;Keith Bradnam;John St. John;Aaron Darling

  • The UCSC Genome Browser Database: 2008 update.

    D. Karolchik;R. M. Kuhn;R. Baertsch;G. P. Barber

  • Nanopore native RNA sequencing of a human poly(A) transcriptome.

    Rachael E. Workman;Alison D. Tang;Paul S. Tang;Miten Jain

  • Variation graph toolkit improves read mapping by representing genetic variation in the reference.

    Erik Garrison;Jouni Sirén;Adam M Novak;Glenn Hickey

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

    Arang Rhie;Shane A. McCarthy;Olivier Fedrigo;Joana Damas

Frequent Co-Authors

David Haussler
David Haussler University of California, Santa Cruz
Erik Garrison
Erik Garrison University of Tennessee Health Science Center
Mark Diekhans
Mark Diekhans University of California, Santa Cruz
Evan E. Eichler
Evan E. Eichler University of Washington
Richard Durbin
Richard Durbin University of Cambridge
Paul Flicek
Paul Flicek The Jackson Laboratory
Daniel R. Zerbino
Daniel R. Zerbino European Bioinformatics Institute
Thomas M. Keane
Thomas M. Keane European Bioinformatics Institute
W. James Kent
W. James Kent University of California, Santa Cruz

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