E R Tillier

Summary

Affiliation: University of Toronto
Country: Canada

Publications

  1. ncbi SIMPROT: using an empirically determined indel distribution in simulations of protein evolution
    Andy Pang
    Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
    BMC Bioinformatics 6:236. 2005
  2. ncbi The accuracy of several multiple sequence alignment programs for proteins
    Paulo A S Nuin
    Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, University Health Network, 101 College St, M5G 1L7, Toronto, Ontario, Canada
    BMC Bioinformatics 7:471. 2006
  3. ncbi A new, fast algorithm for detecting protein coevolution using maximum compatible cliques
    Alex Rodionov
    The Edward S, Rogers Sr, Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada
    Algorithms Mol Biol 6:17. 2011
  4. ncbi The human protein coevolution network
    Elisabeth R M Tillier
    Department of Medical Biophysics, University of Toronto, Ontario Cancer Institute, University Health Network, Canada
    Genome Res 19:1861-71. 2009
  5. ncbi Codep: maximizing co-evolutionary interdependencies to discover interacting proteins
    Elisabeth R M Tillier
    Cancer Genomics and Proteomics, Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
    Proteins 63:822-31. 2006
  6. ncbi The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes
    E R Tillier
    Department of Molecular and Medical Genetics, University of Toronto, 1 King s College Circle, Toronto, Canada M5S 1A8
    J Mol Evol 50:249-57. 2000
  7. ncbi Genome rearrangement by replication-directed translocation
    E R Tillier
    Department of Molecular and Medical Genetics, University of Toronto, Toronto, Canada
    Nat Genet 26:195-7. 2000
  8. ncbi Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments
    Elisabeth R M Tillier
    Ontario Cancer Institute, University Health Network, Suite 703, 620 University Avenue, Toronto, Ontario, Canada M5G 2M9
    Bioinformatics 19:750-5. 2003
  9. ncbi Replication orientation affects the rate and direction of bacterial gene evolution
    E R Tillier
    Department of Molecular and Medical Genetics, University of Toronto, 1 King s College Circle, Toronto, Canada, M5S 1A8
    J Mol Evol 51:459-63. 2000
  10. ncbi Aligning two RNA secondary structures with l-block
    Zhuozhi Wang
    Ontario Cancer Institute, University Health Network, Canada
    Biomol Eng 24:321-6. 2007

Collaborators

Detail Information

Publications15

  1. ncbi SIMPROT: using an empirically determined indel distribution in simulations of protein evolution
    Andy Pang
    Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
    BMC Bioinformatics 6:236. 2005
    ..General protein evolution models help determine the baseline expectations for the evolution of sequences, and they have been extensively useful in sequence analysis and for the computer simulation of artificial sequence data sets...
  2. ncbi The accuracy of several multiple sequence alignment programs for proteins
    Paulo A S Nuin
    Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, University Health Network, 101 College St, M5G 1L7, Toronto, Ontario, Canada
    BMC Bioinformatics 7:471. 2006
    ..The "true" alignment is usually unknown due to the incomplete knowledge of the evolutionary history of the sequences, making it difficult to gauge the relative accuracy of the programs...
  3. ncbi A new, fast algorithm for detecting protein coevolution using maximum compatible cliques
    Alex Rodionov
    The Edward S, Rogers Sr, Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada
    Algorithms Mol Biol 6:17. 2011
    ..abstract:..
  4. ncbi The human protein coevolution network
    Elisabeth R M Tillier
    Department of Medical Biophysics, University of Toronto, Ontario Cancer Institute, University Health Network, Canada
    Genome Res 19:1861-71. 2009
    ..These most strongly coevolving proteins suggest interactions that have been maintained over long periods of evolutionary time, and that are thus likely to be of fundamental importance to cellular function...
  5. ncbi Codep: maximizing co-evolutionary interdependencies to discover interacting proteins
    Elisabeth R M Tillier
    Cancer Genomics and Proteomics, Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
    Proteins 63:822-31. 2006
    ..A program implementing our method, Codep, is freely available to academic users from our website: http://www.uhnresearch.ca/labs/tillier/...
  6. ncbi The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes
    E R Tillier
    Department of Molecular and Medical Genetics, University of Toronto, 1 King s College Circle, Toronto, Canada M5S 1A8
    J Mol Evol 50:249-57. 2000
    ....
  7. ncbi Genome rearrangement by replication-directed translocation
    E R Tillier
    Department of Molecular and Medical Genetics, University of Toronto, Toronto, Canada
    Nat Genet 26:195-7. 2000
    ..Our observations suggest that replication has a major role in directing genome evolution...
  8. ncbi Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments
    Elisabeth R M Tillier
    Ontario Cancer Institute, University Health Network, Suite 703, 620 University Avenue, Toronto, Ontario, Canada M5G 2M9
    Bioinformatics 19:750-5. 2003
    ..The effectiveness of the method was verified using computer simulations and then applied to predict functional interactions between amino acids in the Pfam database of alignments...
  9. ncbi Replication orientation affects the rate and direction of bacterial gene evolution
    E R Tillier
    Department of Molecular and Medical Genetics, University of Toronto, 1 King s College Circle, Toronto, Canada, M5S 1A8
    J Mol Evol 51:459-63. 2000
    ....
  10. ncbi Aligning two RNA secondary structures with l-block
    Zhuozhi Wang
    Ontario Cancer Institute, University Health Network, Canada
    Biomol Eng 24:321-6. 2007
    ..In this paper, we present an algorithm which circumvents this problem. Instead of finding an optimal alignment with predefined gap opening penalty, the algorithm finds the optimal alignment with exact number of aligned blocks...
  11. ncbi Empirical models for substitution in ribosomal RNA
    Andrew D Smith
    Department of Medical Biophysics, University of Toronto, and Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
    Mol Biol Evol 21:419-27. 2004
    ..In addition, the models are useful for simulating the evolution of RNA sequence and structure simultaneously...
  12. ncbi A transition probability model for amino acid substitutions from blocks
    Shalini Veerassamy
    Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
    J Comput Biol 10:997-1010. 2003
    ..Our model is directly derived from, and thus compatible with, the BLOSUM matrices. The model has the additional advantage of being easily implemented...
  13. ncbi Regional covariation and its application for predicting protein contact patches
    Yongbai Xu
    Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
    Proteins 78:548-58. 2010
    ....
  14. ncbi Loss and gain of GroEL in the Mollicutes
    Gregory W Clark
    Ontario Cancer Institute, University Health Network and Department of Medical Biophysics, University of Toronto, 5 354 MaRS TMDT, 101 College St, Toronto, ON M5G 1L7, Canada
    Biochem Cell Biol 88:185-94. 2010
    ..Furthermore, we propose that the presence of GroEL in Mycoplasma may be required for invasion of host tissue, suggesting that GroEL may act as an adhesin-invasin...
  15. ncbi A fast and flexible approach to oligonucleotide probe design for genomes and gene families
    Shengzhong Feng
    Institute of Computing Technology, Chinese Academy of Sciences, China
    Bioinformatics 23:1195-202. 2007
    ..The existing strategies developed for DNA probe design, geared toward identifying specific sequences, are not suitable due to the lack of coverage, flexibility and efficiency necessary for applications in metagenomics...