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bookmarks

publications

(22)   

• Generating consensus sequences from partial order multiple sequence alignment graphs
  Christopher Lee Bioinformatics19(8):999--1008May2003.
  to Gene Algorithms, Humans, Consensus Software, Analysis, Alignment, Sequence DNA, Expression Profiling, by dzerbino and 1 other person on Sep 17, 2007, 8:19 PM
  BibTeX 
• ARACHNE: a whole-genome shotgun assembler
  Serafim Batzoglou and David B Jaffe and Ken Stanley and Jonathan Butler and Sante Gnerre and Evan Mauceli and Bonnie Berger and Jill P Mesirov and Eric S Lander Genome Res12(1):177--89Jan2002.
  to Saccharomyces Drosophila Algorithms, influenzae, melanogaster, Genome, Alignment, Sequence Fungal, Humans Software, Consensus Haemophilus Human, Bacterial, Animals, Mapping, cerevisiae, Sequence, Contig by dzerbino on Sep 17, 2007, 8:19 PM
  BibTeX 
• Minimus: a fast, lightweight genome assembler
  Daniel D Sommer and Arthur L Delcher and Steven L Salzberg and Mihai Pop BMC BioinformaticsFeb2007.
  to Sequence, Design, Molecular DNA, Sequence Analysis, Algorithms, Data, Interface Software Mapping, Alignment, Chromosome Base Software, User-Computer by dzerbino on Sep 17, 2007, 8:19 PM
  BibTeX 
• PCAP: a whole-genome assembly program
  Xiaoqiu Huang and Jianmin Wang and Srinivas Aluru and Shiaw-Pyng Yang and LaDeana Hillier Genome Res13(9):2164--70Sep2003.
  to Genome, Software, Contig Sequence Humans Alignment, Algorithms, Mice, Computational Animals, Mapping, Biology, by dzerbino on Sep 17, 2007, 8:19 PM
  BibTeX 
• A novel method for multiple alignment of sequences with repeated and shuffled elements
  Benjamin Raphael and Degui Zhi and Haixu Tang and Pavel Pevzner Genome Res14(11):2336--46Nov2004.
  to Homology, Acid Sequence Protein, Amino Databases, Alignment, Algorithms, Analysis, Software, Genetic, by dzerbino on Sep 17, 2007, 8:19 PM
  BibTeX 
• Multiple sequence alignment using partial order graphs
  Christopher Lee and Catherine Grasso and Mark F Sharlow Bioinformatics18(3):452--64Mar2002.
  to Expressed Tags, Molecular Alignment, Glucose-1-Phosphate Sensitivity Proteins, Homology, Models, Plant Sequence Time Adenylyltransferase, Control Base Data, Quality Genetic, Algorithms, Messenger, Sequence, Humans, Software, Nucleotidyltransferases, Factors, Specificity, RNA, Statistical, and Databases, DNA, by dzerbino and 1 other person on Sep 17, 2007, 8:19 PM
  BibTeX 
• De novo repeat classification and fragment assembly
  Pavel A Pevzner and Paul A Pevzner and Haixu Tang and Glenn Tesler Genome Res14(9):1786--96Sep2004.
  to Repetitive Linkage Algorithms, (Genetics), Contig Nucleic Human, Chromosomes, Family Humans, Analysis, Computational Acid, Mapping, Genome, Artificial, Multigene Cluster Sequences, Biology, Sequence Alignment, Bacterial, by dzerbino and 1 other person on Sep 17, 2007, 8:19 PM
  BibTeX 
• ProbCons: Probabilistic consistency-based multiple sequence alignment
  Chuong B Do and Mahathi S P Mahabhashyam and Michael Brudno and Serafim Batzoglou Genome Res15(2):330--40Feb2005.
  to Alignment, Variation Acid Sequence, Biology, Databases, Software, Software Sequence Molecular Benchmarking, (Genetics) Computational Algorithms, Data, Protein, Validation, Amino by dzerbino on Sep 17, 2007, 8:19 PM
  BibTeX 
• Fragment assembly with short reads
  Mark Chaisson and Pavel Pevzner and Haixu Tang Bioinformatics20(13):2067--74Sep2004.
  to Contig Mapping, Sequence Feasibility DNA, Analysis, Gene Data, Base Molecular Profiling, Expression Algorithms, Studies, Alignment, by dzerbino and 1 other person on Sep 17, 2007, 8:19 PM
  BibTeX 
• The fragment assembly string graph
  Eugene W Myers BioinformaticsSep2005.
  to Data, Mapping Chromosome DNA Sequence Analysis, Fragmentation, Base Algorithms, Sequence, Molecular DNA, by dzerbino and 2 other people on Sep 17, 2007, 8:19 PM
  BibTeX 
• Genome-scale evolution: reconstructing gene orders in the ancestral species
  Guillaume Bourque and Pavel A Pevzner Genome Res12(1):26--36Jan2002.
  to Animals, Rearrangement, Algorithms, Gene Genetic, Cats, Chromosomes, Human, Genome, Mice, Models, Order, Humans, Molecular, Chromosomes Evolution, by dzerbino and 2 other people on Sep 17, 2007, 8:19 PM
  BibTeX 
• Assembling millions of short DNA sequences using SSAKE
  Ren'e L Warren and Granger G Sutton and Steven J M Jones and Robert A Holt Bioinformatics23(4):500--1Feb2007.
  to Software, Base Mapping, Sequence Sequence, Chromosome Contig Molecular Algorithms, Analysis, DNA, Data, Mapping by dzerbino and 1 other person on Sep 17, 2007, 8:19 PM
  BibTeX 
• A whole-genome assembly of Drosophila
  E W Myers and G G Sutton and A L Delcher and I M Dew and D P Fasulo and M J Flanigan and S A Kravitz and C M Mobarry and K H Reinert and K A Remington and E L Anson and R A Bolanos and H H Chou and C M Jordan and A L Halpern and S Lonardi and E M Beasley and R C Brandon and L Chen and P J Dunn and Z Lai and Y Liang and D R Nusskern and M Zhan and Q Zhang and X Zheng and G M Rubin and M D Adams and J C Venter Science287(5461):2196--204Mar2000.
  to Chromosome Sequences, Analysis, Computational Sites, DNA, Acid, Insect, Tagged Algorithms, melanogaster, Physical Sequence Molecular Contig Genes, Nucleic Genome, Biology Heterochromatin, Euchromatin, Drosophila Chromatin, Animals, Data, Repetitive Mapping, by dzerbino on Sep 17, 2007, 8:19 PM
  BibTeX 
• Efficiently detecting polymorphisms during the fragment assembly process
  Daniel Fasulo and Aaron Halpern and Ian Dew and Clark Mobarry BioinformaticsJan2002.
  to Profiling, Analysis, Fragment Fragmentation Polymorphism, Molecular Algorithms, Data, Alignment, Base Restriction Gene Sequence Sequence, (Genetics), Variation DNA, DNA Genetic, Expression Length, Consensus by dzerbino and 1 other person on Sep 17, 2007, 8:19 PM
  BibTeX 
• Occupancy modeling of coverage distribution for whole genome shotgun DNA sequencing
  Michael C Wendl Bull Math Biol68(1):179--96Jan2006.
  to Humans, Models, Sequence Statistical Genome, Analysis, Genomics, Algorithms, DNA, Animals, by dzerbino on Sep 17, 2007, 8:19 PM
  BibTeX 
• Gene maps linearization using genomic rearrangement distances
  Guillaume Blin and Eric Blais and Danny Hermelin and Pierre Guillon and Mathieu Blanchette and Nadia El-Mabrouk J Comput Biol14(4):394--407May2007.
  to Biology, Analysis, Genome, Computational Software DNA, Genomics, Sequence Algorithms, by dzerbino on Sep 17, 2007, 8:19 PM
  BibTeX 
• SSAHA: a fast search method for large DNA databases
  Z Ning and A J Cox and J C Mullikin Genome Res11(10):1725--9Oct2001.
  to Alignment, Base Composition, Systems, and Factual, Sequence, Sequence DNA, Software, Management Specificity Sensitivity Databases, Algorithms, Database by dzerbino on Sep 17, 2007, 8:19 PM
  BibTeX 
• A pseudo-boolean framework for computing rearrangement distances between genomes with duplicates
  S'ebastien Angibaud and Guillaume Fertin and Irena Rusu and St'ephane Vialette J Comput Biol14(4):379--93May2007.
  to Duplication, Genome, Software, Algorithms, Computational Sequence Gene Gammaproteobacteria, DNA, Bacterial Analysis, Biology, by dzerbino on Sep 17, 2007, 8:19 PM
  BibTeX 
• Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model
  R Agarwala and S Batzoglou and V Danc'ik and S E Decatur and S Hannenhalli and M Farach and S Muthukrishnan and S Skiena J Comput Biol4(3):275--96Jan1997.
  to Protein Molecular, Folding, Models, Conformation, Chemical Algorithms, by dzerbino on Sep 17, 2007, 8:19 PM
  BibTeX 
• An Eulerian path approach to DNA fragment assembly
  P A Pevzner and H Tang and M S Waterman Proc Natl Acad Sci USA98(17):9748--53Aug2001.
  to Algorithms, jejuni, Software, DNA, meningitidis, Genome, Theoretical, lactis Contig Lactococcus Campylobacter Alignment, Analysis, Sequence Neisseria Mapping, Bacterial, Models, by dzerbino and 1 other person on Sep 17, 2007, 8:19 PM
  BibTeX