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A method for probing the mutational landscape
of amyloid structure. |
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Charles W. O'Donnell, Jerome Waldispuhl, Mieszko Lis, Randal
Halfmann, Srinivas Devadas, Susan Lindquist and Bonnie
Berger |
|
| 19th
Annual International Conference on Intelligent Systems for Molecular
Biology & 19th European Conference on Computational Biology ISMB/ECCB
2011, Bioinformatics, to appear. |
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Structure-based prediction reveals capping motifs that
inhibit
β-helix aggregation. |
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Allen W. Bryan, Jr., Jennifer Starner-Kreinbrink,
Raghavendra Hosur, Patricia Clark and Bonnie Berger |
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Proceedings of the National Academy of Sciences, to appear. |
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Opposing effects of glutamine and asparagine govern prion
formation by intrinsically disordered proteins. |
|
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Randal Halfmann, Simon Alberti, Rajaraman Krishnan, Nicholas
Lyle, Charles W. O'Donnell, Oliver D. King, Bonnie Berger,
Rohit V. Pappu and Susan Lindquist |
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Molecular Cell, to appear. |
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Efficient traversal of protein folding pathways using
ensemble models |
|
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Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Bonnie
Berger and Jerome Waldispuhl |
|
| Lecture
Notes in Computer Science (2011) Vol. 6577, 408-423
doi:10.1007/978-3-642-20036-6_38 |
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Sparse estimation for structural variability |
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Raghavendra Hosur, Rohit Singh and Bonnie Berger |
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Algorithms for Molecular Biology (2010) Selected for fast-track
publication in AMB from WABI 2010, in press. |
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Struct2Net: A web service to predict protein-protein
interactions using a structure-based approach |
|
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Rohit Singh, Daniel Park, Jinbo Xu, Raghavendra Hosur, and
Bonnie Berger |
|
| Nucleic
Acids Research (2010) 38 (suppl 2): W508-W515
http://dx.doi.org/10.1093/nar/gkq481
|
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iWRAP: An interface threading approach with application to
prediction of cancer related protein-protein interactions |
|
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Raghavendra Hosur, Jinbo Xu, Jadwiga Bienkowska, and Bonnie
Berger |
|
| Journal
of Molecular Biology (2010)
http://dx.doi.org/10.1016/j.jmb.2010.11.025 |
|
Markov random fields reveal an N-terminal double
beta-propeller motif as part of a bacterial hybrid
two-component sensor system |
|
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Matt Menke, Bonnie Berger* and Lenore Cowen |
|
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Proceedings of the National Academy of Sciences (2010) www.pnas.org/cgi/doi/10.1073/pnas.0909950107 |
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RNAmutants: a web server to explore the mutational landscape
of RNA secondary structures |
|
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Jerome Waldispuhl, Srinivas Devadas, Bonnie Berger* and
Peter Clote* |
|
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Nucleic Acids Research (2009) 37:46, W281-W286 |
|
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Simultaneous alignment and folding of protein sequences |
|
| Jerome Waldispuhl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen and Bonnie Berger |
|
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| Inverting the
viterbi algorithm: An abstract framework for structure design |
|
| Michael Schnall-Levin, Leonid Chindelevitch and Bonnie Berger |
|
| Proceedings of the 25th International Conference on Machine Learning (2008). |
|
| http://portal.acm.org/citation.cfm?id=1390270 |
|
Predicting and annotating catalytic residues: An information
theoretic approach |
|
| |
Beckett Sterner, Rohit Singh and Bonnie Berger |
|
| |
Journal of Computational Biology 14 no. 8, 1-16. |
|
| 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. |
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abstract |
bibTeX citation |
publisher's site |
|
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 |
|
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| 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. |
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|
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 |
| 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) 53:4, 533 -557. |
|
|
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 |
|
| 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 xtructural motif recognition with zpplication to recognizing
beta trefoils |
|
|
Matthew Menke, Eben Scanlon, Jonathan King, Lenore Cowen, and Bonnie Berger |
|
|
Journal of Computational Biology (2005) 12 no. 6, 777-795. |
|
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abstract |
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 |
| |
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 |
| |
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 |
| |
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 |
| |
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 |
| |
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.
|
|
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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.
|
|
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abstract |
bibTeX citation |
publisher's site |
| |
Algorithms for
protein structural motif recognition |
|
|
|
| | Journal of Computational Biology (1995) 2 no. 1, 125-138.
|
|
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abstract |
bibTeX citation |
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| |
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.
|
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abstract |
bibTeX citation |
publisher's site |
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