Franco P Preparata

Summary

Affiliation: Brown University
Country: USA

Publications

  1. doi request reprint On contigs and coverage
    Franco P Preparata
    Computer Science Department, Brown University, Providence, RI 02912, USA
    J Comput Biol 20:424-32. 2013
  2. ncbi request reprint Sequencing-by-hybridization at the information-theory bound: an optimal algorithm
    F P Preparata
    Computer Science Department, Brown University, Providence, RI 02912 1910, USA
    J Comput Biol 7:621-30. 2000
  3. ncbi request reprint DNA sequencing by hybridization using semi-degenerate bases
    Franco P Preparata
    Computer Science Department, Brown University, Providence, RI 02912 1910, USA
    J Comput Biol 11:753-65. 2004
  4. ncbi request reprint Quick, practical selection of effective seeds for homology search
    Franco P Preparata
    Computer Science Department, Brown University, Providence, RI 02912 1910, USA
    J Comput Biol 12:1137-52. 2005
  5. ncbi request reprint Sequencing-by-hybridization revisited: the analog-spectrum proposal
    Franco P Preparata
    Computer Science Department, Brown University, 115 Waterman Street, Providence, RI 02912 1910, USA
    IEEE/ACM Trans Comput Biol Bioinform 1:46-52. 2004
  6. ncbi request reprint A novel approach to the detection of genomic approximate tandem repeats in the Levenshtein metric
    Nevzat Onur Domaniç
    Department of Computer Science, Brown University, Providence, Rhode Island 02912, USA
    J Comput Biol 14:873-91. 2007
  7. ncbi request reprint Sequencing by hybridization by cooperating direct and reverse spectra
    Samuel A Heath
    Computer Science Department, Brown University, 115 Waterman Street, Providence, RI 02912 1910, USA
    J Comput Biol 10:499-508. 2003
  8. ncbi request reprint Adaptive control of hybridization noise in DNA sequencing-by-hybridization
    Hon Wai Leong
    School of Computing, National University of Singapore, Singapore
    J Bioinform Comput Biol 3:79-98. 2005
  9. doi request reprint Spectrum-based de novo repeat detection in genomic sequences
    Huy Hoang Do
    Department of Computer Science, National University of Singapore, Singapore
    J Comput Biol 15:469-87. 2008

Collaborators

Detail Information

Publications9

  1. doi request reprint On contigs and coverage
    Franco P Preparata
    Computer Science Department, Brown University, Providence, RI 02912, USA
    J Comput Biol 20:424-32. 2013
    ..The second is a detailed analysis of the effect of replacing the hypothesis of fixed-length genomic fragments with that of an arbitrary distribution of lengths over a finite interval...
  2. ncbi request reprint Sequencing-by-hybridization at the information-theory bound: an optimal algorithm
    F P Preparata
    Computer Science Department, Brown University, Providence, RI 02912 1910, USA
    J Comput Biol 7:621-30. 2000
    ..Moreover, this performance is achieved while maintaining running time linear in the target sequence length...
  3. ncbi request reprint DNA sequencing by hybridization using semi-degenerate bases
    Franco P Preparata
    Computer Science Department, Brown University, Providence, RI 02912 1910, USA
    J Comput Biol 11:753-65. 2004
    ..While universal bases represent the ultimate goal of sequencing by hybridization, semidegenerate natural bases are the most effective known substitute...
  4. ncbi request reprint Quick, practical selection of effective seeds for homology search
    Franco P Preparata
    Computer Science Department, Brown University, Providence, RI 02912 1910, USA
    J Comput Biol 12:1137-52. 2005
    ..While the challenging mathematical question of characterizing optimal search seeds remains open, we believe that our eminently efficient and effective approach represents a satisfactory solution from a practitioner's viewpoint...
  5. ncbi request reprint Sequencing-by-hybridization revisited: the analog-spectrum proposal
    Franco P Preparata
    Computer Science Department, Brown University, 115 Waterman Street, Providence, RI 02912 1910, USA
    IEEE/ACM Trans Comput Biol Bioinform 1:46-52. 2004
    ..One important conclusion is that accurate biochemical measurements are pivotal to the success of SBH. The theoretical proposal presented in this paper should be a convincing stimulus for the needed biotechnological work...
  6. ncbi request reprint A novel approach to the detection of genomic approximate tandem repeats in the Levenshtein metric
    Nevzat Onur Domaniç
    Department of Computer Science, Brown University, Providence, Rhode Island 02912, USA
    J Comput Biol 14:873-91. 2007
    ..The algorithm is available at www.cs.brown.edu/people/domanic/tandem/...
  7. ncbi request reprint Sequencing by hybridization by cooperating direct and reverse spectra
    Samuel A Heath
    Computer Science Department, Brown University, 115 Waterman Street, Providence, RI 02912 1910, USA
    J Comput Biol 10:499-508. 2003
    ..In other words, tandem-spectrum reconstruction is the best known technique for sequencing by hybridization...
  8. ncbi request reprint Adaptive control of hybridization noise in DNA sequencing-by-hybridization
    Hon Wai Leong
    School of Computing, National University of Singapore, Singapore
    J Bioinform Comput Biol 3:79-98. 2005
    ..In addition, the experimental algorithmic speed-ups of the multithreshold approach are explained in terms of the interaction amongst the different threshold regimes...
  9. doi request reprint Spectrum-based de novo repeat detection in genomic sequences
    Huy Hoang Do
    Department of Computer Science, National University of Singapore, Singapore
    J Comput Biol 15:469-87. 2008
    ..An executable program can be downloaded at http://sagri.comp.nus.edu.sg...