Bonnie Berger

	2012
73		Sebastian Will, Michael Yu, Bonnie Berger: Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAs. RECOMB 2012: 341
72		Noah Daniels, Raghavendra Hosur, Bonnie Berger, Lenore J. Cowen: SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone. Bioinformatics 28(9): 1216-1222 (2012)
	2011
71		Leonid Chindelevitch, Aviv Regev, Bonnie Berger: Metabolic Network Analysis Demystified. RECOMB 2011: 31-33
70		Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger, Jérôme Waldispühl: Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models. RECOMB 2011: 408-423
69		Yanhui Hu, Ian Flockhart, Arunachalam Vinayagam, Clemens Bergwitz, Bonnie Berger, Norbert Perrimon, Stephanie E. Mohr: An Integrative Approach to Ortholog Prediction for Disease-Focused and Other Functional Studies. BMC Bioinformatics 12: 357 (2011)
68		Charles W. O'Donnell, Jérôme Waldispühl, Mieszko Lis, Randal Halfmann, Srinivas Devadas, Susan Lindquist, Bonnie Berger: A method for probing the mutational landscape of amyloid structure. Bioinformatics [ISMB/ECCB] 27(13): 34-42 (2011)
67		Daniel Park, Rohit Singh, Michael Baym, Chung-Shou Liao, Bonnie Berger: IsoBase: a database of functionally related proteins across PPI networks. Nucleic Acids Research 39(Database-Issue): 295-300 (2011)
	2010
66		Bonnie Berger: Research in Computational Molecular Biology, 14th Annual International Conference, RECOMB 2010, Lisbon, Portugal, April 25-28, 2010. Proceedings Springer 2010
65		Leonid Chindelevitch, Chung-Shou Liao, Bonnie Berger: Local Optimization for Global Alignment of Protein Interaction Networks. Pacific Symposium on Biocomputing 2010: 123-132
64		Raghavendra Hosur, Rohit Singh, Bonnie Berger: Sparse Estimation for Structural Variability. WABI 2010: 13-27
63		Rohit Singh, Daniel Park, Jinbo Xu, Raghavendra Hosur, Bonnie Berger: Struct2Net: a web service to predict protein-protein interactions using a structure-based approach. Nucleic Acids Research 38(Web-Server-Issue): 508-515 (2010)
	2009
62		Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger: Simultaneous Alignment and Folding of Protein Sequences. RECOMB 2009: 339-355
61		Chung-Shou Liao, Kanghao Lu, Michael Baym, Rohit Singh, Bonnie Berger: IsoRankN: spectral methods for global alignment of multiple protein networks. Bioinformatics 25(12): (2009)
60		Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote: RNAmutants: a web server to explore the mutational landscape of RNA secondary structures. Nucleic Acids Research 37(Web-Server-Issue): 281-286 (2009)
59		Allen W. Bryan Jr., Matthew Menke, Lenore J. Cowen, Susan Lindquist, Bonnie Berger: BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis. PLoS Computational Biology 5(3): (2009)
	2008
58		Michael Schnall-Levin, Leonid Chindelevitch, Bonnie Berger: Inverting the Viterbi algorithm: an abstract framework for structure design. ICML 2008: 904-911
57		Rohit Singh, Jinbo Xu, Bonnie Berger: Global Alignment of Multiple Protein Interaction Networks. Pacific Symposium on Biocomputing 2008: 303-314
56		Michael Baym, Chris Bakal, Norbert Perrimon, Bonnie Berger: High-Resolution Modeling of Cellular Signaling Networks. RECOMB 2008: 257-271
55		Bonnie Berger, Rohit Singh, Jinbo Xu: Graph algorithms for biological systems analysis. SODA 2008: 142-151
54		Vinay Pulim, Bonnie Berger, Jadwiga R. Bienkowska: Optimal contact map alignment of protein-protein interfaces. Bioinformatics 24(20): 2324-2328 (2008)
53		Matthew Menke, Bonnie Berger, Lenore Cowen: Matt: Local Flexibility Aids Protein Multiple Structure Alignment. PLoS Computational Biology 4(1): (2008)
52		Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote: Efficient Algorithms for Probing the RNA Mutation Landscape. PLoS Computational Biology 4(8): (2008)
	2007
51		David Sontag, Rohit Singh, Bonnie Berger: Probabilistic Modeling of Systematic Errors in Two-Hybrid Experiments. Pacific Symposium on Biocomputing 2007: 445-457
50		Vinay Pulim, Jadwiga R. Bienkowska, Bonnie Berger: Lthreader: Prediction of Ligand-Receptor Interactions Using Localized Threading. Pacific Symposium on Biocomputing 2007: 64-75
49		Rohit Singh, Jinbo Xu, Bonnie Berger: Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology. RECOMB 2007: 16-31
48		Jinbo Xu, Feng Jiao, Bonnie Berger: A Parameterized Algorithm for Protein Structure Alignment. Journal of Computational Biology 14(5): 564-577 (2007)
47		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		Rohit Singh, Jinbo Xu, Bonnie Berger: Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction. Pacific Symposium on Biocomputing 2006: 403-414
45		Jinbo Xu, Feng Jiao, Bonnie Berger: A Parameterized Algorithm for Protein Structure Alignment. RECOMB 2006: 488-499
44		Jinbo Xu, Bonnie Berger: Fast and accurate algorithms for protein side-chain packing. J. ACM 53(4): 533-557 (2006)
43		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		Jinbo Xu, Feng Jiao, Bonnie Berger: A Tree-Decomposition Approach to Protein Structure Prediction. CSB 2005: 247-256
41		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		Rohit Singh, Bonnie Berger: ChainTweak: Sampling from the Neighbourhood of a Protein Conformation. Pacific Symposium on Biocomputing 2005: 54-65
39		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		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		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		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		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		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		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		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		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		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		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		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		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		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		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	Rolf Backofen	[62]
3	Chris Bakal	[56]
4	E. Banks	[26]
5	Ziv Bar-Joseph	[41]
6	Serafim Batzoglou	[26] [29] [31] [32]
7	Michael Baym	[56] [61] [67]
8	William S. Beebee	[29]
9	Clemens Bergwitz	[69]
10	Jadwiga R. Bienkowska	[50] [54]
11	Bruce Birren	[36] [37]
12	Phil Bradley	[33] [34] [35]
13	Martin L. Brady	[15]
14	Donna J. Brown	[15]
15	Allen W. Bryan Jr.	[59]
16	Leonid Chindelevitch	[58] [65] [71]
17	Peter Clote	[43] [52] [60]
18	Lenore Cowen (Lenore J. Cowen)	[7] [8] [9] [10] [11] [14] [17] [23] [33] [34] [38] [39] [53] [59] [72]
19	Noah Daniels	[72]
20	Srinivas Devadas	[52] [60] [62] [68] [70]
21	Ian Flockhart	[69]
22	David K. Gifford	[41]
23	Randal Halfmann	[68]
24	G. W. Hoest	[27]
25	Raghavendra Hosur	[63] [64] [72]
26	Yanhui Hu	[69]
27	Feng Jiao	[42] [45] [48]
28	Manolis Kamvysselis	[36]
29	Manolis Kellis	[37]
30	Peter S. Kim	[35]
31	Jonathan King	[33] [34] [38] [39]
32	Jonathan A. King	[30]
33	Jon M. Kleinberg	[18] [28]
34	Daniel J. Kleitman	[26] [29]
35	Eric S. Lander	[26] [29] [31] [32] [36] [37]
36	Frank Thomson Leighton (Tom Leighton)	[15] [18] [24] [25] [28]
37	Chung-Shou Liao	[61] [65] [67]
38	Susan Lindquist	[59] [68]
39	Mieszko Lis	[68]
40	Kanghao Lu	[61]
41	Matthew Menke	[33] [34] [38] [39] [53] [59]
42	Jill P. Mesirov	[31] [32]
43	Stephanie E. Mohr	[69]
44	Charles W. O'Donnell	[62] [68] [70]
45	Lior Pachter	[26] [29] [31]
46	Nathan Palmer	[41]
47	Daniel Park	[63] [67]
48	Nick Patterson	[36] [37]
49	J. R. Paulson	[27]
50	David Peleg	[8] [9] [10] [11] [17] [23]
51	Norbert Perrimon	[56] [69]
52	Vinay Pulim	[50] [54]
53	Aviv Regev	[71]
54	John Rompel	[1] [2] [3] [5] [12]
55	Eben Scanlon	[38]
56	Michael Schnall-Levin	[58]
57	Russell Schwartz	[30]
58	Solomon Shenker	[70]
59	Peter W. Shor	[1] [4] [12] [21] [27] [30]
60	Mona Singh	[20] [22]
61	Rohit Singh	[40] [41] [46] [47] [49] [51] [55] [57] [61] [63] [64] [67]
62	David Sontag	[51]
63	Valentin I. Spitkovsky	[26] [29]
64	Beckett Sterner	[47]
65	Jean-Marc Steyaert	[43]
66	Arunachalam Vinayagam	[69]
67	Jérôme Waldispühl	[43] [52] [60] [62] [68] [70]
68	Sebastian Will	[62] [73]
69	David Bruce Wilson	[16]
70	Jinbo Xu	[42] [44] [45] [46] [48] [49] [55] [57] [63]
71	Michael Yu	[73]

Colors in the list of coauthors

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