2008 | ||
---|---|---|
56 | EE | Michael Schnall-Levin, Leonid Chindelevitch, Bonnie Berger: Inverting the Viterbi algorithm: an abstract framework for structure design. ICML 2008: 904-911 |
55 | EE | Rohit Singh, Jinbo Xu, Bonnie Berger: Global Alignment of Multiple Protein Interaction Networks. Pacific Symposium on Biocomputing 2008: 303-314 |
54 | EE | Michael Baym, Chris Bakal, Norbert Perrimon, Bonnie Berger: High-Resolution Modeling of Cellular Signaling Networks. RECOMB 2008: 257-271 |
53 | EE | Bonnie Berger, Rohit Singh, Jinbo Xu: Graph algorithms for biological systems analysis. SODA 2008: 142-151 |
52 | EE | Vinay Pulim, Bonnie Berger, Jadwiga R. Bienkowska: Optimal contact map alignment of protein-protein interfaces. Bioinformatics 24(20): 2324-2328 (2008) |
2007 | ||
51 | EE | David Sontag, Rohit Singh, Bonnie Berger: Probabilistic Modeling of Systematic Errors in Two-Hybrid Experiments. Pacific Symposium on Biocomputing 2007: 445-457 |
50 | EE | Vinay Pulim, Jadwiga R. Bienkowska, Bonnie Berger: Lthreader: Prediction of Ligand-Receptor Interactions Using Localized Threading. Pacific Symposium on Biocomputing 2007: 64-75 |
49 | EE | Rohit Singh, Jinbo Xu, Bonnie Berger: Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology. RECOMB 2007: 16-31 |
48 | EE | Jinbo Xu, Feng Jiao, Bonnie Berger: A Parameterized Algorithm for Protein Structure Alignment. Journal of Computational Biology 14(5): 564-577 (2007) |
47 | EE | Beckett Sterner, Rohit Singh, Bonnie Berger: Predicting and Annotating Catalytic Residues: An Information Theoretic Approach. Journal of Computational Biology 14(8): 1058-1073 (2007) |
2006 | ||
46 | EE | Rohit Singh, Jinbo Xu, Bonnie Berger: Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction. Pacific Symposium on Biocomputing 2006: 403-414 |
45 | EE | Jinbo Xu, Feng Jiao, Bonnie Berger: A Parameterized Algorithm for Protein Structure Alignment. RECOMB 2006: 488-499 |
44 | EE | Jinbo Xu, Bonnie Berger: Fast and accurate algorithms for protein side-chain packing. J. ACM 53(4): 533-557 (2006) |
43 | EE | Jérôme Waldispühl, Bonnie Berger, Peter Clote, Jean-Marc Steyaert: transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels. Nucleic Acids Research 34(Web-Server-Issue): 189-193 (2006) |
2005 | ||
42 | EE | Jinbo Xu, Feng Jiao, Bonnie Berger: A Tree-Decomposition Approach to Protein Structure Prediction. CSB 2005: 247-256 |
41 | EE | 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. ICML 2005: 832-839 |
40 | EE | Rohit Singh, Bonnie Berger: ChainTweak: Sampling from the Neighbourhood of a Protein Conformation. Pacific Symposium on Biocomputing 2005: 54-65 |
39 | EE | 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. Journal of Computational Biology 12(6): 777-795 (2005) |
2004 | ||
38 | EE | 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. RECOMB 2004: 298-307 |
37 | EE | Manolis Kellis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric S. Lander: Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery. Journal of Computational Biology 11(2/3): 319-355 (2004) |
2003 | ||
36 | EE | Manolis Kamvysselis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric S. Lander: Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species. RECOMB 2003: 157-16 |
2002 | ||
35 | EE | Phil Bradley, Peter S. Kim, Bonnie Berger: Trilogy: discovery of sequence-structure patterns across diverse proteins. RECOMB 2002: 77-88 |
34 | Lenore Cowen, Phil Bradley, Matthew Menke, Jonathan King, Bonnie Berger: Predicting the Beta-Helix Fold from Protein Sequence Data. Journal of Computational Biology 9(2): 261-276 (2002) | |
2001 | ||
33 | EE | Phil Bradley, Lenore Cowen, Matthew Menke, Jonathan King, Bonnie Berger: Predicting the beta-helix fold from protein sequence data. RECOMB 2001: 59-67 |
2000 | ||
32 | EE | Serafim Batzoglou, Bonnie Berger, Jill P. Mesirov, Eric S. Lander: Sequencing a genome by walking with clone-end sequences: a mathematical analysis (abstract). RECOMB 2000: 45 |
31 | EE | Serafim Batzoglou, Lior Pachter, Jill P. Mesirov, Bonnie Berger, Eric S. Lander: Human and mouse gene structure: comparative analysis and application to exon prediction. RECOMB 2000: 46-53 |
30 | Bonnie Berger, Jonathan A. King, Russell Schwartz, Peter W. Shor: Local rule mechanism for selecting icosahedral shell geometry. Discrete Applied Mathematics 104(1-3): 97-111 (2000) | |
1999 | ||
29 | EE | 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. RECOMB 1999: 285-294 |
28 | EE | Bonnie Berger, Jon M. Kleinberg, Frank Thomson Leighton: Reconstructing a Three-Dimensional Model with Arbitrary Errors. J. ACM 46(2): 212-235 (1999) |
27 | Bonnie Berger, G. W. Hoest, J. R. Paulson, Peter W. Shor: On the Structure of the Scaffolding Core of Bacteriophage T4. Journal of Computational Biology 6(1): 1-12 (1999) | |
26 | Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, E. Banks, Eric S. Lander, Daniel J. Kleitman, Bonnie Berger: A Dictionary-Based Approach for Gene Annotation. Journal of Computational Biology 6(3/4): (1999) | |
1998 | ||
25 | EE | Bonnie Berger, Frank Thomson Leighton: Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete. RECOMB 1998: 30-39 |
24 | Bonnie Berger, Frank Thomson Leighton: Protein Folding in the Hydrophobic-Hydrophilic(HP) Model is NP-Complete. Journal of Computational Biology 5(1): 27-40 (1998) | |
23 | Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg: Near-Linear Time Construction of Sparse Neighborhood Covers. SIAM J. Comput. 28(1): 263-277 (1998) | |
1997 | ||
22 | EE | Bonnie Berger, Mona Singh: An iterative method for improved protein structural motif recognition. RECOMB 1997: 37-46 |
21 | Bonnie Berger, Peter W. Shor: Tight Bounds for the Maximum Acyclic Subgraph Problem. J. Algorithms 25(1): 1-18 (1997) | |
20 | Bonnie Berger, Mona Singh: An Iterative Method for Improved Protein Structural Motif Recognition. Journal of Computational Biology 4(3): 261-274 (1997) | |
19 | Bonnie Berger: The Fourth Moment Method. SIAM J. Comput. 26(4): 1188-1207 (1997) | |
1996 | ||
18 | EE | Bonnie Berger, Jon M. Kleinberg, Frank Thomson Leighton: Reconstructing a Three-Dimensional Model with Arbitrary Errors. STOC 1996: 449-458 |
17 | Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg: Fast Distributed Network Decompositions and Covers. J. Parallel Distrib. Comput. 39(2): 105-114 (1996) | |
1995 | ||
16 | Bonnie Berger, David Bruce Wilson: Improved Algorithms for Protein Motif Recognition. SODA 1995: 58-67 | |
15 | EE | Bonnie Berger, Martin L. Brady, Donna J. Brown, Frank Thomson Leighton: Nearly Optimal Algorithms and Bounds for Multilayer Channel Routing. J. ACM 42(2): 500-542 (1995) |
14 | Bonnie Berger, Lenore Cowen: Scheduling with Concurrency-Based Constraints. J. Algorithms 18(1): 98-123 (1995) | |
13 | Bonnie Berger: Algorithms for Protein Structural Motif Recognition. Journal of Computational Biology 2(1): 125-138 (1995) | |
1994 | ||
12 | Bonnie Berger, John Rompel, Peter W. Shor: Efficient NC Algorithms for Set Cover with Applications to Learning and Geometry. J. Comput. Syst. Sci. 49(3): 454-477 (1994) | |
11 | Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg: Low-Diameter Graph Decomposition Is in NC. Random Struct. Algorithms 5(3): 441-452 (1994) | |
1993 | ||
10 | Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg: Near-Linear Cost Sequential and Distribured Constructions of Sparse Neighborhood Covers FOCS 1993: 638-647 | |
1992 | ||
9 | Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg: Fast Network Decomposition (Extended Abstract). PODC 1992: 169-177 | |
8 | Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg: Low-Diameter Graph Decomposition is in NC. SWAT 1992: 83-93 | |
1991 | ||
7 | Bonnie Berger, Lenore Cowen: Complexity Results and Algorithms for { <, <=, = }-Constrained Scheduling. SODA 1991: 137-147 | |
6 | Bonnie Berger: The Fourth Moment Method. SODA 1991: 373-383 | |
5 | EE | Bonnie Berger, John Rompel: Simulating (log c n)-Wise Independence in NC. J. ACM 38(4): 1026-1046 (1991) |
1990 | ||
4 | Bonnie Berger, Peter W. Shor: Approximation Algorithms for the Maximum Acyclic Subgraph Problem. SODA 1990: 236-243 | |
3 | Bonnie Berger, John Rompel: A Better Performance Guarantee for Approximate Graph Coloring. Algorithmica 5(3): 459-466 (1990) | |
1989 | ||
2 | Bonnie Berger, John Rompel: Simulating (log ^c n)-wise Independence in NC FOCS 1989: 2-7 | |
1 | Bonnie Berger, John Rompel, Peter W. Shor: Efficient NC Algorithms for Set Cover with Applications to Learning and Geometry FOCS 1989: 54-59 |