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Bonnie Berger: [Publications] [Author Rank by year] [Co-authors] [Prefers] [Cites] [Cited by]

Publications of Author

  1. Jinbo Xu, Feng Jiao, Bonnie Berger
    A Tree-Decomposition Approach to Protein Structure Prediction. [Citation Graph (0, 0)][DBLP]
    CSB, 2005, pp:247-256 [Conf]
  2. Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg
    Near-Linear Cost Sequential and Distribured Constructions of Sparse Neighborhood Covers [Citation Graph (0, 0)][DBLP]
    FOCS, 1993, pp:638-647 [Conf]
  3. Bonnie Berger, John Rompel
    Simulating (log ^c n)-wise Independence in NC [Citation Graph (0, 0)][DBLP]
    FOCS, 1989, pp:2-7 [Conf]
  4. Bonnie Berger, John Rompel, Peter W. Shor
    Efficient NC Algorithms for Set Cover with Applications to Learning and Geometry [Citation Graph (0, 0)][DBLP]
    FOCS, 1989, pp:54-59 [Conf]
  5. Rohit Singh, Nathan Palmer, David K. Gifford, Bonnie Berger, Ziv Bar-Joseph
    Active learning for sampling in time-series experiments with application to gene expression analysis. [Citation Graph (0, 0)][DBLP]
    ICML, 2005, pp:832-839 [Conf]
  6. Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg
    Fast Network Decomposition (Extended Abstract). [Citation Graph (0, 0)][DBLP]
    PODC, 1992, pp:169-177 [Conf]
  7. Rohit Singh, Bonnie Berger
    ChainTweak: Sampling from the Neighbourhood of a Protein Conformation. [Citation Graph (0, 0)][DBLP]
    Pacific Symposium on Biocomputing, 2005, pp:54-65 [Conf]
  8. Rohit Singh, Jinbo Xu, Bonnie Berger
    Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction. [Citation Graph (0, 0)][DBLP]
    Pacific Symposium on Biocomputing, 2006, pp:403-414 [Conf]
  9. Phil Bradley, Lenore Cowen, Matthew Menke, Jonathan King, Bonnie Berger
    Predicting the beta-helix fold from protein sequence data. [Citation Graph (0, 0)][DBLP]
    RECOMB, 2001, pp:59-67 [Conf]
  10. Phil Bradley, Peter S. Kim, Bonnie Berger
    Trilogy: discovery of sequence-structure patterns across diverse proteins. [Citation Graph (0, 0)][DBLP]
    RECOMB, 2002, pp:77-88 [Conf]
  11. Serafim Batzoglou, Bonnie Berger, Jill P. Mesirov, Eric S. Lander
    Sequencing a genome by walking with clone-end sequences: a mathematical analysis (abstract). [Citation Graph (0, 0)][DBLP]
    RECOMB, 2000, pp:45- [Conf]
  12. Serafim Batzoglou, Lior Pachter, Jill P. Mesirov, Bonnie Berger, Eric S. Lander
    Human and mouse gene structure: comparative analysis and application to exon prediction. [Citation Graph (0, 0)][DBLP]
    RECOMB, 2000, pp:46-53 [Conf]
  13. Bonnie Berger, Frank Thomson Leighton
    Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete. [Citation Graph (0, 0)][DBLP]
    RECOMB, 1998, pp:30-39 [Conf]
  14. Bonnie Berger, Mona Singh
    An iterative method for improved protein structural motif recognition. [Citation Graph (0, 0)][DBLP]
    RECOMB, 1997, pp:37-46 [Conf]
  15. Manolis Kamvysselis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric S. Lander
    Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species. [Citation Graph (0, 0)][DBLP]
    RECOMB, 2003, pp:157-16 [Conf]
  16. Matthew Menke, Eben Scanlon, Jonathan King, Bonnie Berger, Lenore Cowen
    Wrap-and-pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils. [Citation Graph (0, 0)][DBLP]
    RECOMB, 2004, pp:298-307 [Conf]
  17. Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, William S. Beebee, Eric S. Lander, Bonnie Berger, Daniel J. Kleitman
    A dictionary based approach for gene annotation. [Citation Graph (0, 0)][DBLP]
    RECOMB, 1999, pp:285-294 [Conf]
  18. Jinbo Xu, Feng Jiao, Bonnie Berger
    A Parameterized Algorithm for Protein Structure Alignment. [Citation Graph (0, 0)][DBLP]
    RECOMB, 2006, pp:488-499 [Conf]
  19. Rohit Singh, Jinbo Xu, Bonnie Berger
    Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology. [Citation Graph (0, 0)][DBLP]
    RECOMB, 2007, pp:16-31 [Conf]
  20. Bonnie Berger
    The Fourth Moment Method. [Citation Graph (0, 0)][DBLP]
    SODA, 1991, pp:373-383 [Conf]
  21. Bonnie Berger, Lenore Cowen
    Complexity Results and Algorithms for { <, <=, = }-Constrained Scheduling. [Citation Graph (0, 0)][DBLP]
    SODA, 1991, pp:137-147 [Conf]
  22. Bonnie Berger, Peter W. Shor
    Approximation Algorithms for the Maximum Acyclic Subgraph Problem. [Citation Graph (0, 0)][DBLP]
    SODA, 1990, pp:236-243 [Conf]
  23. Bonnie Berger, David Bruce Wilson
    Improved Algorithms for Protein Motif Recognition. [Citation Graph (0, 0)][DBLP]
    SODA, 1995, pp:58-67 [Conf]
  24. Bonnie Berger, Jon M. Kleinberg, Frank Thomson Leighton
    Reconstructing a Three-Dimensional Model with Arbitrary Errors. [Citation Graph (0, 0)][DBLP]
    STOC, 1996, pp:449-458 [Conf]
  25. Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg
    Low-Diameter Graph Decomposition is in NC. [Citation Graph (0, 0)][DBLP]
    SWAT, 1992, pp:83-93 [Conf]
  26. Bonnie Berger, John Rompel
    A Better Performance Guarantee for Approximate Graph Coloring. [Citation Graph (0, 0)][DBLP]
    Algorithmica, 1990, v:5, n:3, pp:459-466 [Journal]
  27. Bonnie Berger, Jonathan A. King, Russell Schwartz, Peter W. Shor
    Local rule mechanism for selecting icosahedral shell geometry. [Citation Graph (0, 0)][DBLP]
    Discrete Applied Mathematics, 2000, v:104, n:1-3, pp:97-111 [Journal]
  28. Bonnie Berger, Martin L. Brady, Donna J. Brown, Frank Thomson Leighton
    Nearly Optimal Algorithms and Bounds for Multilayer Channel Routing. [Citation Graph (0, 0)][DBLP]
    J. ACM, 1995, v:42, n:2, pp:500-542 [Journal]
  29. Bonnie Berger, Jon M. Kleinberg, Frank Thomson Leighton
    Reconstructing a Three-Dimensional Model with Arbitrary Errors. [Citation Graph (0, 0)][DBLP]
    J. ACM, 1999, v:46, n:2, pp:212-235 [Journal]
  30. Bonnie Berger, John Rompel
    Simulating (log c n)-Wise Independence in NC. [Citation Graph (0, 0)][DBLP]
    J. ACM, 1991, v:38, n:4, pp:1026-1046 [Journal]
  31. Jinbo Xu, Bonnie Berger
    Fast and accurate algorithms for protein side-chain packing. [Citation Graph (0, 0)][DBLP]
    J. ACM, 2006, v:53, n:4, pp:533-557 [Journal]
  32. Bonnie Berger, Lenore Cowen
    Scheduling with Concurrency-Based Constraints. [Citation Graph (0, 0)][DBLP]
    J. Algorithms, 1995, v:18, n:1, pp:98-123 [Journal]
  33. Bonnie Berger, Peter W. Shor
    Tight Bounds for the Maximum Acyclic Subgraph Problem. [Citation Graph (0, 0)][DBLP]
    J. Algorithms, 1997, v:25, n:1, pp:1-18 [Journal]
  34. Bonnie Berger
    Algorithms for Protein Structural Motif Recognition. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 1995, v:2, n:1, pp:125-138 [Journal]
  35. Bonnie Berger, G. W. Hoest, J. R. Paulson, Peter W. Shor
    On the Structure of the Scaffolding Core of Bacteriophage T4. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 1999, v:6, n:1, pp:1-12 [Journal]
  36. Bonnie Berger, Frank Thomson Leighton
    Protein Folding in the Hydrophobic-Hydrophilic(HP) Model is NP-Complete. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 1998, v:5, n:1, pp:27-40 [Journal]
  37. Lenore Cowen, Phil Bradley, Matthew Menke, Jonathan King, Bonnie Berger
    Predicting the Beta-Helix Fold from Protein Sequence Data. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 2002, v:9, n:2, pp:261-276 [Journal]
  38. Bonnie Berger, Mona Singh
    An Iterative Method for Improved Protein Structural Motif Recognition. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 1997, v:4, n:3, pp:261-274 [Journal]
  39. Manolis Kellis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric S. Lander
    Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 2004, v:11, n:2/3, pp:319-355 [Journal]
  40. Matthew Menke, Jonathan King, Bonnie Berger, Lenore Cowen
    Wrap-and-Pack: A New Paradigm for Beta Structural Motif Recognition with Application to Recognizing Beta Trefoils. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 2005, v:12, n:6, pp:777-795 [Journal]
  41. Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, E. Banks, Eric S. Lander, Daniel J. Kleitman, Bonnie Berger
    A Dictionary-Based Approach for Gene Annotation. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 1999, v:6, n:3/4, pp:- [Journal]
  42. Bonnie Berger, John Rompel, Peter W. Shor
    Efficient NC Algorithms for Set Cover with Applications to Learning and Geometry. [Citation Graph (0, 0)][DBLP]
    J. Comput. Syst. Sci., 1994, v:49, n:3, pp:454-477 [Journal]
  43. Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg
    Fast Distributed Network Decompositions and Covers. [Citation Graph (0, 0)][DBLP]
    J. Parallel Distrib. Comput., 1996, v:39, n:2, pp:105-114 [Journal]
  44. Jérôme Waldispühl, Bonnie Berger, Peter Clote, Jean-Marc Steyaert
    transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2006, v:34, n:Web-Server-Issue, pp:189-193 [Journal]
  45. Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg
    Low-Diameter Graph Decomposition Is in NC. [Citation Graph (0, 0)][DBLP]
    Random Struct. Algorithms, 1994, v:5, n:3, pp:441-452 [Journal]
  46. Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg
    Near-Linear Time Construction of Sparse Neighborhood Covers. [Citation Graph (0, 0)][DBLP]
    SIAM J. Comput., 1998, v:28, n:1, pp:263-277 [Journal]
  47. Bonnie Berger
    The Fourth Moment Method. [Citation Graph (0, 0)][DBLP]
    SIAM J. Comput., 1997, v:26, n:4, pp:1188-1207 [Journal]

  48. Inverting the Viterbi algorithm: an abstract framework for structure design. [Citation Graph (, )][DBLP]


  49. Lthreader: Prediction of Ligand-Receptor Interactions Using Localized Threading. [Citation Graph (, )][DBLP]


  50. Probabilistic Modeling of Systematic Errors in Two-Hybrid Experiments. [Citation Graph (, )][DBLP]


  51. Global Alignment of Multiple Protein Interaction Networks. [Citation Graph (, )][DBLP]


  52. High-Resolution Modeling of Cellular Signaling Networks. [Citation Graph (, )][DBLP]


  53. Simultaneous Alignment and Folding of Protein Sequences. [Citation Graph (, )][DBLP]


  54. Graph algorithms for biological systems analysis. [Citation Graph (, )][DBLP]


  55. Sparse Estimation for Structural Variability. [Citation Graph (, )][DBLP]


  56. Optimal contact map alignment of protein-protein interfaces. [Citation Graph (, )][DBLP]


  57. IsoRankN: spectral methods for global alignment of multiple protein networks. [Citation Graph (, )][DBLP]


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