|
|
 |
|
2008 Publications
| |
High-Resolution Modeling of Cellular Signaling Networks. |
|
| |
Michael Baym, Chris Bakal, Norbert Perrimon and Bonnie Berger |
|
| |
Proceedings of the 12th Annual International Conference on Research in Computational Molecular Biology (2008) LNBI 4955: 257-271 |
|
| abstract |
http://dx.doi.org/10.1007/978-3-540-78839-3_22 |
| Inverting the Viterbi Algorithm: An Abstract Framework for Structure Design. |
|
| Michael Schnall-Levin, Leonid Chindelevitch and Bonnie Berger |
|
| The 25th International Conference on Machine Learning (2008). In press |
|
| abstract |
|
| Efficient algorithms for probing the RNA mutation landscape. |
|
| Jerome Waldispühl, Srini Devadas, Bonnie Berger and Peter Clote |
|
| PLoS Computational Biology. In press |
|
| abstract |
|
|
|
|
|
|
| |
2007 Publications |
|
| Predicting and Annotating Catalytic Residues: An Information Theoretic Approach. |
|
| |
Beckett Sterner, Rohit Singh and Bonnie Berger |
|
| |
Journal of Computational Biology 14 , no. 8: 1058 |
|
| abstract |
bibTeX citation |
publisher's site |
| Influence Flow: Integrating Pathway-specific RNAi data and Protein
Interaction Data. |
|
| |
Rohit Singh and Bonnie Berger |
|
| |
15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)
& 6th European Conference on Computational Biology (ECCB), July 2007 Please cite this paper as "Personal Communication", as per the guidelines of the PLoS track at ISMB |
|
| abstract |
bibTeX citation |
publisher's site |
| Pairwise Global Alignment of Protein Interaction Networks By Matching Neighborhood Topology. |
|
| |
Rohit Singh, Jinbo Xu and Bonnie Berger |
|
| |
Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology (2007): Lecture Notes in Computer Science , 4453: 16-31 |
|
| abstract |
bibTeX citation |
publisher's site |
| Lthreader: Prediction of Ligand-Receptor Interactions Using Localized Threading. |
|
| Vinay Pulim, Jadwiga Bienkowska and Bonnie Berger |
|
| Pacific Symposium on Biocomputing (2007), 12:64-75 |
|
| abstract |
bibTeX citation |
publisher's site |
| Automated real time constant-specificity surveillance for disease outbreaks. |
|
| Shannon C Wieland, John S Brownstein, Bonnie Berger and Kenneth D Mandl |
|
| BMC Medical Informatics and Decision Making (2007), 7:15 |
|
| abstract |
|
|
| Density-equalizing Euclidean minimum spanning trees for the dectection of all disease cluster shapes. |
|
| Shannon C Wieland, John S Brownstein, Bonnie Berger and Kenneth D Mandl |
|
| Proceedings of the National Academy of Sciences (2007) 104:9404-9409 |
|
| abstract |
|
|
| A Parameterized Algorithm for Protein Structure Alignment. |
| Jinbo Xu, Feng Jiao and Bonnie Berger |
|
| Journal of Computational Biology (2007) 14 (5): 564-577 Also appeared in RECOMB 2006 |
|
| abstract |
|
|
| Modeling Ensembles of Transmembrane Beta-barrels Proteins |
|
| Jerome Waldispühl*, Charles W O'Donnell*, Srinivas Devadas, Peter Clote and Bonnie Berger (* authors equally contributed) |
|
| Proteins: Structure, Function, and Bioinformatics 71, no. 3:1097-1112 |
|
| abstract |
dx.doi.org/doi:10.1002/prot.21788 |
| Pertactin Beta-Helix Folding Mechanism Suggests Common Themes
for the Secretion and Folding of Autotransporter Proteins. |
|
| |
Mirco Junker, Christopher Schuster, Andrew McDonnell, Kelli Sorg, Mary Finn, Bonnie Berger and Patricia Clark |
|
| |
Proceedings of the National Academy of Sciences (2006), 103: 4918-4923 |
|
|
abstract |
bibTeX citation |
publisher's site |
| Struct2Net: Integrating Structure Into Protein-Protein Interaction Prediction. |
|
| |
Rohit Singh, Jinbo Xu, and Bonnie Berger |
|
| |
In Proceedings of the 11th Pacific Symposium on Biocomputing (2006): 403-414 |
|
|
abstract |
bibTeX citation |
Publisher's Site
|
| Paircoil2: Improved prediction of coiled coils from sequence. |
|
| |
Andrew V. McDonnell, Taijiao Jiang, Amy E. Keating and Bonnie Berger |
|
| |
Bioinformatics (2006), 23, 356-358 |
|
|
abstract |
bibTeX citation |
Publisher's Site |
| Herpesviral protein networks and their interaction with the human
proteome. |
|
| |
Peter Uetz, Yu-An Dong, Christine Zeretzke, Christine Atzler, Armin Baiker,
Bonnie Berger, Seesandra Rajagopala, Maria Roupelieva, Dietlind Rose, Even Fossum
and Jürgen Haas |
|
| |
Science (2006), 13 January, 311: 239-242; published online 7 December 2005 [DOI: 10.1126/science.1116804] (in Reports) |
|
|
abstract |
bibTeX citation |
Publisher's Site |
| Fold recognition and accurate sequence-structure alignment of sequences directing beta-sheet proteins. |
|
| |
Andrew V. McDonnell, Matthew Menke, Nathan Palmer, Jonathan King, Lenore Cowen and Bonnie Berger |
|
| |
Proteins: Structure, Function, and Bioinformatics, (2006), 63, 976-985 |
|
|
abstract |
bibTeX citation |
|
| A Parameterized Algorithm for Protein Structure Alignment. |
|
| |
Jinbo Xu, Feng Jiao and Bonnie Berger |
|
| |
In Proceedings of the 10th Annual International Conference on Research in Computational Molecular Biology RECOMB (2006), 488-499. |
|
|
abstract |
bibTeX citation |
Publisher's Site |
| Predicting Transmembrane β-barrels and Inter-strand Residue
Interactions from Sequence.
|
|
| |
Jerome Waldispühl, Bonnie Berger, Peter Clote and Jean-Marc Steyaert |
|
| |
PROTEINS: Structure, function and Bioinformatics (2006), 65, 61-74 |
|
|
abstract |
bibTeX citation |
Publisher's Site |
| transFold: a Web Server for Predicting Transmembrane β-barrels and
Inter-strand Residue Interactions from Sequence. |
|
| |
Jerome Waldispühl, Bonnie Berger, Peter Clote and Jean-Marc Steyaert |
|
| |
Nucleic Acids Research (Web Server Issue) (2006), 34, W189-W193 |
|
|
abstract |
bibTeX citation |
Publisher's Site |
| Fast and Accurate Algorithms for Protein Side-Chain Packing. |
|
| |
Jinbo Xu and Bonnie Berger |
|
| |
Journal of the ACM (2006), 53, Issue 4 |
|
|
abstract |
bibTeX citation |
|
| Constant specificity surveillance for real-time outbreak detection. |
|
| |
Shannon C. Wieland, Bonnie Berger and Ken D. Mandl |
|
| |
MMWR Morb Mortal Wkly Rep (2005): 54 Suppl, 206 |
|
|
abstract |
bibTeX citation |
|
| A Tree Decomposition Approach to Protein Structure Prediction. |
|
| |
Jinbo Xu and Bonnie Berger |
|
| |
Proceedings of IEEE CSB 2005 (2005): 247-256 |
|
|
abstract |
bibTeX citation |
|
| Local rule simulations of capsid assembly. |
|
| |
Russell Schwartz, Peter W. Shor and Bonnie Berger |
|
| |
Journal of Theoretical Medicine (June 2005): 6, no. 2: 81-85 |
|
|
abstract |
bibTeX citation |
|
| Active Learning for Sampling in Time-Series Experiments: With
Applications to Gene Expression Analysis. |
|
| |
Rohit Singh, Nathan Palmer, David Gifford, Bonnie Berger, and Ziv
Bar-Joseph |
|
| |
Proceedings of the 22nd Annual International Conference on Machine
Learning (2005) 833-840 |
|
|
abstract |
bibTeX citation |
|
| ChainTweak: Sampling from the Neighbourhood of a Protein Conformation. |
|
| | Rohit Singh and Bonnie Berger |
|
| |
In Proceedings of the 10th Pacific Symposium on Biocomputation (2005): 52-63 |
|
|
abstract |
bibTeX citation |
|
| |
Wrap-and-Pack: A New Paradigm for Beta Structural Motif Recognition with Application to Recognizing Beta Trefoils. |
|
|
Matthew Menke, Eben Scanlon, Jonathan King, Lenore Cowen, and Bonnie Berger |
|
|
Journal of Computational Biology (2005) 11, no. 6: 777-795 |
|
| abstract |
bibTeX citation |
|
| |
Methods in Comparative Genomics: Genome Correspondence, Gene Identification, and Motif Discovery.
|
|
|
Manolis Kellis, Nick Patterson, Bruce Birren, Bonnie Berger , and Eric S. Lander |
|
|
Journal of Computational Biology (2004) 11, no.2-3: 319-355 |
|
| |
bibTeX citation |
|
| |
MSARi: Multiple sequence alignments for statistical detection of RNA secondary structure.
|
|
|
Alex Coventry, Daniel J. Kleitman, and Bonnie Berger
|
| |
Proceedings of the National Academy of Sciences (2004) 101, no. 33: 12102-12107 |
|
| abstract |
bibTeX citation |
publisher's site |
|
| 2003 Publications |
| |
| |
Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species. |
|
| | Manolis Kellis (Kamvysselis), Nick Patterson , Bruce Birren , Bonnie Berger, and Eric Lander
|
|
| | In Proceedings of the 7th Annual International Conference on Research in Computational Molecular Biology RECOMB (2003) : 157-166
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
Predicting the Beta-Helix Fold From Protein Sequence Data.
|
|
| | Lenore Cowen, Philip Bradley, Matthew Menke, Jonathan King, and Bonnie Berger
|
|
| | J of Computational Biology (2002) 9: 261-276
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
ARACHNE: A Whole-Genome Shotgun Assembler.
|
|
| | Serafim Batzoglou
, David B. Jaffe
, Ken Stanley
, Jonathan Butler
, Sante Gnerre
, Evan Mauceli
, Bonnie Berger
, Jill P. Mesirov
, and Eric S. Lander
|
|
| | Genome Research
(2002
) 12
, no. 1
: 177
-189
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
TRILOGY: Discovery of sequence-structure patterns across diverse proteins. |
|
| | Philip Bradley, Peter S. Kim, and Bonnie Berger
|
|
| | Proceedings of the National Academy of Sciences (2002) 99: 8500-8505
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
BETAWRAP: Successful prediction of parallel Beta-helices from primary sequence reveals an association with many microbial pathogens.
|
|
| | Philip Bradley, Lenore Cowen, Matthew Menke, Jonathan King, and Bonnie Berger
|
|
| | Proceedings of the National Academy of Sciences (2001) 98, no. 26: 14819-14824
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
Local Rule Mechanism for Selecting Icosahedral Shell Geometry. |
|
| | Bonnie Berger, Jonathan King, Russell S. Schwartz, and Peter W. Shor
|
|
| | Discrete Applied Mathematics (2000) 104, no. 1: 97-111
|
|
|
abstract |
bibTeX citation |
|
| |
'Local Rules' Theory Applied to Polyomavirus Polymorphic Capsid Assemblies. |
|
| | Russell S. Schwartz, Robert L. Garcea, and Bonnie Berger
|
|
| | Virology (2000) 268, no. 2: 461-470
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction. |
|
| | Serafim Batzoglou, Lior Pachter, Jill Mesirov, Bonnie Berger, and Eric S. Lander
|
|
| | Genome Research (2000) 10: 950-958
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
Sequencing a Genome by Walking with Clone-end Sequences: A Mathematical Analysis. |
|
| | Serafim Batzoglou, Bonnie Berger, Jill Mesirov, and Eric S. Lander
|
|
| | Genome Research (1999) 9, no. 12: 1163-1174
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
On the Structure of the Scaffolding Core of Bacteriophage T4.
|
|
| | Bonnie Berger, G.W.~Hoest, J.~Paulson, and Peter W. Shor
|
|
| | Journal of Computational Biology (1999) 6, no. 1: 1-12
|
|
|
|
bibTeX citation |
|
| |
Reconstructing a Three-Dimensional Model with Arbitrary Errors. |
|
| | Bonnie Berger, Jon Kleinberg, and Tom Leighton
|
|
| | Journal of the Association for Computing Machinery (1999) 46, no. 2: 212-235
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
LearnCoil-VMF: Computational Evidence for Coiled-coil-like Motifs in Many Viral Membrane Fusion Proteins |
|
| | Mona Singh, Bonnie Berger, and Peter S. Kim
|
|
| | Journal of Molecular Biology (1999) 290, no. 5: 1031-1041
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
A Dictionary Based Approach for Gene Annotation.
|
|
| | Lior Pachter, Serafim Batzoglou, Valentin Spitkovsky, Eric Banks, Eric S. Lander, Daniel J. Kleitman, and Bonnie Berger
|
|
| | Journal of Computational Biology (1999) 6, no. 3: 419-430
|
|
|
|
bibTeX citation |
|
| |
Near-Linear Cost Construction of Sparse Neighborhood Covers.
|
|
| | Baruch Awerbuch, Bonnie Berger, Lenore Cowen, and David Peleg
|
|
| | SIAM Journal on Computing (1998) 28, no. 1: 263-277
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
On the Structure of the Scaffolding Core of Bacteriophage T4 and its Role in Head-Length Determination.
|
|
| | Bonnie Berger and Peter W. Shor
|
|
| | Journal of Structural Biology (1998) 121, no. 3: 285-294
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
Local Rules Simulation of the Kinetics of Virus Capsid Self-Assembly.
|
|
| | Russell Schwartz, Peter W. Shor, Peter E. Prevelige, and Bonnie Berger
|
|
| | Biophysical Journal (1998) 75, no. 1: 2626-2636
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
Computational Learning Reveals Coiled Coil-like Motifs in Histidine Kinase Linker Domains.
|
|
| | Mona Singh, Bonnie Berger, Peter S. Kim, J.M.~Berger, and A.G.~Cochran
|
|
| | Proceedings of the National Academy of Science USA (1998) 95, no. 6: 2738-2743
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
Protein Folding in the Hydrophobic-Hydrophilic (HP) Model is NP-Complete. |
|
| | Bonnie Berger and Tom Leighton
|
|
| | Journal of Computational Biology (1998) 5, no. 1: 27-40
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
Recent Developments in Computational Gene Recognition. |
|
| | Serafim Batzoglou, Bonnie Berger, Daniel J. Kleitman, Eric S. Lander, and Lior Pachter
|
|
| | Documenta Mathematica: Journal der Deutschen Mathematiker-Vereinigung (1998) Extra Volume ICM I: 649-658
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
Topological Modeling of Cascade Amorphization in Network Structures Using Local Rules.
|
|
| | L.W.~Hobbs, Esther Jesurum, Vinay Pulim, and Bonnie Berger
|
|
| | Material Science and Engineering (1998) A 253, no. 1: 16-29
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
Topological Modeling of Topologically-Disordered Tetrahedral Structures Using Local Approaches. |
|
| | Esther Jesurum, Vinay Pulim, Bonnie Berger, and L.~Hobbs
|
|
| | Materials Science Forum (1997) 239: 37-40
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
MultiCoil: A Program for Predicting Two and Three Stranded Coiled Coils.
|
|
| | Ethan Wolf, Peter S. Kim, and Bonnie Berger
|
|
| | Protein Science (1997) 6, no. 6: 1179-1189
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
An Iterative Method for Improved Protein Structural Motif Recognition.
|
|
| | Bonnie Berger and Mona Singh
|
|
| | Journal of Computational Biology (1997) 4, no. 3: 261-273
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
Fast Distributed Network Decomposition. |
|
| | Baruch Awerbuch, Bonnie Berger, Lenore Cowen, and David Peleg
|
|
| | Journal of Parallel and Distributed Computing (1996) 39, no. 2: 105-114
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
Structural Freedom, Topological Disorder, and the Irradiation-Induced Amorphization of Ceramic Structures.
|
|
| | L.W. Hobbs, A.N. Sreeram, Esther Jesurum, and Bonnie Berger
|
|
| | Nuclear Instruments and Methods in Physics Research Section B (1996) 116, no. 1: 17-25
|
|
|
abstract |
bibTeX citation |
|
| |
Algorithms for Protein Structural Motif Recognition. |
|
|
|
| | Journal of Computational Biology (1995) 2, no. 1: 125-138
|
|
|
abstract |
bibTeX citation |
|
| |
Nearly Optimal Algorithms and Bounds for Multilayer Channel Routing.
|
|
| | Bonnie Berger, Martin Brady, Donna Brown, and Tom Leighton
|
|
| | Journal of the Association for Computing Machinery (1995) 42, no. 2: 500-542
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
Predicting Coiled Coils by Use of Pairwise Residue Correlations. |
|
| | Bonnie Berger, David B. Wilson, Ethan Wolf, Theodore Tonchev, Maria Milla, and Peter S. Kim
|
|
| | Proceedings of the National Academy of Science USA (1995) 92: 8259-8263
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
A Local Rule Based Theory of Virus Shell Assembly. |
|
| | Bonnie Berger, Peter W. Shor, Lisa Tucker-Kellogg, and Jonathan King
|
|
| | Proceedings of the National Academy of Science USA (1994) 91, no. 16: 7732-7736
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
Low Diameter Graph Decomposition is in NC. |
|
| | Baruch Awerbuch, Bonnie Berger, Lenore Cowen, and David Peleg
|
|
| | Random Structures and Algorithms (1994) 5, no. 3: 441-452
|
|
|
abstract |
bibTeX citation |
publisher's site |
| |
Efficient NC Algorithms for Set Cover with Applications to Learning and Geometry.
|
|
| | Bonnie Berger, John Rompel, and Peter W. Shor
|
|
| | Journal of Computer and System Sciences (1994) 49, no. 3: 454-477
|
|
|
abstract |
bibTeX citation |
|
| |
Simulating (logc n)-Wise Independence in NC.
|
|
| | Bonnie Berger and John Rompel
|
|
| | Journal of the Association for Computing Machinery (1991) 38, no. 4: 1026-1046
|
|
|
abstract |
bibTeX citation |
|
| |
A Better Performance Guarantee for Approximate Graph Coloring. |
|
| | Bonnie Berger and John Rompel
|
|
| | Algorithmica (1990) 5, no. 3: 459-466
|
|
|
abstract |
bibTeX citation |
|
|
|
|
