Bonnie Berger

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

Coauthor Index

1	Baruch Awerbuch	[8] [9] [10] [11] [17] [23]
2	Chris Bakal	[54]
3	E. Banks	[26]
4	Ziv Bar-Joseph	[41]
5	Serafim Batzoglou	[26] [29] [31] [32]
6	Michael Baym	[54]
7	William S. Beebee	[29]
8	Jadwiga R. Bienkowska	[50] [52]
9	Bruce Birren	[36] [37]
10	Phil Bradley	[33] [34] [35]
11	Martin L. Brady	[15]
12	Donna J. Brown	[15]
13	Leonid Chindelevitch	[56]
14	Peter Clote	[43]
15	Lenore Cowen	[7] [8] [9] [10] [11] [14] [17] [23] [33] [34] [38] [39]
16	David K. Gifford	[41]
17	G. W. Hoest	[27]
18	Feng Jiao	[42] [45] [48]
19	Manolis Kamvysselis	[36]
20	Manolis Kellis	[37]
21	Peter S. Kim	[35]
22	Jonathan King	[33] [34] [38] [39]
23	Jonathan A. King	[30]
24	Jon M. Kleinberg	[18] [28]
25	Daniel J. Kleitman	[26] [29]
26	Eric S. Lander	[26] [29] [31] [32] [36] [37]
27	Frank Thomson Leighton (Tom Leighton)	[15] [18] [24] [25] [28]
28	Matthew Menke	[33] [34] [38] [39]
29	Jill P. Mesirov	[31] [32]
30	Lior Pachter	[26] [29] [31]
31	Nathan Palmer	[41]
32	Nick Patterson	[36] [37]
33	J. R. Paulson	[27]
34	David Peleg	[8] [9] [10] [11] [17] [23]
35	Norbert Perrimon	[54]
36	Vinay Pulim	[50] [52]
37	John Rompel	[1] [2] [3] [5] [12]
38	Eben Scanlon	[38]
39	Michael Schnall-Levin	[56]
40	Russell Schwartz	[30]
41	Peter W. Shor	[1] [4] [12] [21] [27] [30]
42	Mona Singh	[20] [22]
43	Rohit Singh	[40] [41] [46] [47] [49] [51] [53] [55]
44	David Sontag	[51]
45	Valentin I. Spitkovsky	[26] [29]
46	Beckett Sterner	[47]
47	Jean-Marc Steyaert	[43]
48	Jérôme Waldispühl	[43]
49	David Bruce Wilson	[16]
50	Jinbo Xu	[42] [44] [45] [46] [48] [49] [53] [55]

Colors in the list of coauthors