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 |