Benedict Paten

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Genome-wide nucleotide-level mammalian ancestor reconstruction
    Benedict Paten
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 18:1829-43. 2008
  2. doi request reprint Cactus graphs for genome comparisons
    Benedict Paten
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California, USA
    J Comput Biol 18:469-81. 2011
  3. pmc A unifying model of genome evolution under parsimony
    Benedict Paten
    University of California, Santa Cruz, 1156 High St, 95064 Santa Cruz, USA
    BMC Bioinformatics 15:206. 2014
  4. pmc Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs
    Benedict Paten
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA
    Genome Res 18:1814-28. 2008
  5. doi request reprint Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment
    Benedict Paten
    Department of Engineering, University of California, Santa Cruz CA, USA
    Bioinformatics 25:295-301. 2009
  6. pmc Cactus: Algorithms for genome multiple sequence alignment
    Benedict Paten
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, CA 95064, USA
    Genome Res 21:1512-28. 2011
  7. pmc HAL: a hierarchical format for storing and analyzing multiple genome alignments
    Glenn Hickey
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz CA 95064, USA
    Bioinformatics 29:1341-2. 2013
  8. pmc Building a pan-genome reference for a population
    Ngan Nguyen
    1 Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California
    J Comput Biol 22:387-401. 2015
  9. pmc The UCSC Genome Browser database: 2015 update
    Kate R Rosenbloom
    Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 43:D670-81. 2015
  10. pmc Alignathon: a competitive assessment of whole-genome alignment methods
    Dent Earl
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA Biomolecular Engineering Department, University of California Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 24:2077-89. 2014

Detail Information

Publications17

  1. pmc Genome-wide nucleotide-level mammalian ancestor reconstruction
    Benedict Paten
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 18:1829-43. 2008
    ..As a first piece of analysis, we attempt to recover "fossilized" ancestral pseudogenes. We confidently find 31 cases in which the ancestral sequence had a more complete sequence than any of the extant sequences...
  2. doi request reprint Cactus graphs for genome comparisons
    Benedict Paten
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California, USA
    J Comput Biol 18:469-81. 2011
    ..Supplementary Material is available at www.liebertonline.com/cmb ...
  3. pmc A unifying model of genome evolution under parsimony
    Benedict Paten
    University of California, Santa Cruz, 1156 High St, 95064 Santa Cruz, USA
    BMC Bioinformatics 15:206. 2014
    ..Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued in isolation...
  4. pmc Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs
    Benedict Paten
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA
    Genome Res 18:1814-28. 2008
    ..Alignments from our pipeline are publicly available within the Ensembl genome browser...
  5. doi request reprint Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment
    Benedict Paten
    Department of Engineering, University of California, Santa Cruz CA, USA
    Bioinformatics 25:295-301. 2009
    ..However, less work has been done in making promising methods that work on the small-scale practically for the alignment of much larger genomic sequences...
  6. pmc Cactus: Algorithms for genome multiple sequence alignment
    Benedict Paten
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, CA 95064, USA
    Genome Res 21:1512-28. 2011
    ..Finally, we make an empirical assessment of Cactus's ability to properly align genes and find interesting cases of intra-gene duplication within the primates...
  7. pmc HAL: a hierarchical format for storing and analyzing multiple genome alignments
    Glenn Hickey
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz CA 95064, USA
    Bioinformatics 29:1341-2. 2013
    ..This loss of information grows with the number of species under comparison, as well as their phylogenetic distance...
  8. pmc Building a pan-genome reference for a population
    Ngan Nguyen
    1 Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California
    J Comput Biol 22:387-401. 2015
    ..In addition, we test the use of a pan-genome for describing variations and as a reference for read mapping. ..
  9. pmc The UCSC Genome Browser database: 2015 update
    Kate R Rosenbloom
    Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 43:D670-81. 2015
    ..As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled. ..
  10. pmc Alignathon: a competitive assessment of whole-genome alignment methods
    Dent Earl
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA Biomolecular Engineering Department, University of California Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 24:2077-89. 2014
    ..We provide all data sets, submissions, and assessment programs for further study and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments...
  11. pmc Comparative assembly hubs: web-accessible browsers for comparative genomics
    Ngan Nguyen
    Center for Biomolecular Sciences and Engineering, CBSE ITI, UC Santa Cruz, 1156 High St, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
    Bioinformatics 30:3293-301. 2014
    ..It is not possible, or necessarily desirable, that the public genome browsers attempt to curate all these data. Instead, a wealth of powerful tools is emerging to empower users to create their own visualizations and browsers...
  12. pmc Accurate reconstruction of insertion-deletion histories by statistical phylogenetics
    Oscar Westesson
    University of California Berkeley and University of California San Francisco Graduate Program in Bioengineering, University of California, Berkeley, California, United States of America
    PLoS ONE 7:e34572. 2012
    ..The algorithm can also be used for alignment-free inference, where the MSA is explicitly summed out of the analysis. As an illustration of our method, we discuss reconstruction of the evolutionary histories of human protein-coding genes...
  13. pmc Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser
    Brian J Raney
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA
    Bioinformatics 30:1003-5. 2014
    ..For the first time, individuals can use the complete browser feature set to view custom datasets without the overhead of setting up and maintaining a mirror...
  14. pmc Assemblathon 1: a competitive assessment of de novo short read assembly methods
    Dent Earl
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA
    Genome Res 21:2224-41. 2011
    ..The simulated benchmark, including the correct answer, the assemblies, and the code that was used to evaluate the assemblies is now public and freely available from http://www.assemblathon.org/...
  15. pmc Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
    Richard E Green
    Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
    Science 346:1254449. 2014
    ....
  16. pmc Meta-alignment with crumble and prune: partitioning very large alignment problems for performance and parallelization
    Krishna M Roskin
    Department of Computer Science, Univ of California, Santa Cruz, USA
    BMC Bioinformatics 12:144. 2011
    ..Both methods partition the problem such that many of the sub-problems can be solved independently. The results are then combined to form a solution to the full alignment problem...
  17. pmc An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons
    Frank M J Jacobs
    1 Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA 2 3 Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098 XH, The Netherlands F M J J Gladstone Institute of Virology and Immunology, San Francisco, California 94158, USA D G Mater Research Institute, University of Queensland, Queensland 4101, Australia A D E
    Nature 516:242-5. 2014
    ....