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Highlighted Publications -
All Publications
(* for corresponding author or † for my student is first author)
2011 Publications
A method for probing the mutational landscape
of amyloid structure. |
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Charles W. O'Donnell, Jerome Waldispühl, Mieszko Lis, Randal
Halfmann, Srinivas Devadas, Susan Lindquist and Bonnie
Berger* |
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19th
Annual International Conference on Intelligent Systems for Molecular
Biology & 19th European Conference on Computational Biology ISMB/ECCB
2011, Bioinformatics, to appear. |
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. |
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. |
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 Waldispühl* |
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Lecture
Notes in Computer Science (2011) Vol. 6577, 408-423
doi:10.1007/978-3-642-20036-6_38 |
Metabolic network analysis demystified |
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Leoind Chindelevich, Aviv Regev and Bonnie Berger* |
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Lecture Notes
in Computer Science, Vol. 6577 ISBN 978-3-642-20035-9
Springer Berlin Heidelberg 2011, p. 31.
doi:10.1007/978-3-642-20036-6_3 |
2010 Publications
Identification of functional elements and regulatory
circuits by drosophila modENCODE |
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Science (2010) 330:6012, 1787-1797
DOI:
10.1126/science.1198374 |
v
Conserved microRNA targeting in drosophila is as widespread
in coding regions as in 3' UTRs |
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Michael Schnall-Levin, Yong Zhao, Norbert Perrimon* and Bonnie Berger* |
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Proceedings of the National Academy of Sciences (2010) 107:36, 15751-15756 |
Phenotype prediction in DREAM5 via regression variants |
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Po-Ru Loh, George Tucker, Michael Yu and Bonnie Berger* |
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Winner, DREAM5 Challenge 3B Competition. Presented at RECOMB 2010
Systems Biology Satellite Conference |
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. |
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* |
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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* |
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Journal
of Molecular Biology (2010)
http://dx.doi.org/10.1016/j.jmb.2010.11.025 |
Inference of RhoGAP/GTPase regulation using single-cell
morphological data from a combinatorial RNAiScreen |
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Oaz Nir, Chris Bakal, Norbert Perrimon and Bonnie Berger* |
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Genome Research
(2010)
20: 372-380
doi:10.1101/gr.101246.109
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Local optimization for the global alignment of protein
interaction networks |
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Leonid Chindelevitch, Chung-Shou Liao and Bonnie Berger* |
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Pacific Symposium on Biocomputing (2010) p.123-132
10.1142/9789814295291_0015 |
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 |
2009 Publications
Large-scale identification of genetic design strategies
using local search |
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Desmond S. Lun, Graham Rockwell, Nicholas J. Guido, Michael
Baym, Jonathan A, Kelner, Bonnie Berger, James E. Galagan
and George M. Church* |
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RNAiCut: automated detection of significant genes from
functional genomic screens |
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Irene Kaplow†, Rohit Singh†, Adam Friedman, Chris Bakal,
Norbert Perrimon* and
Bonnie Berger* |
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Nature Methods (2009) 6 (7):476-7 |
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RNAmutants: a web server to explore the mutational landscape
of RNA secondary structures |
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Jerome Waldispühl, 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 |
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Jerome Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen and Bonnie Berger* |
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A practical
platform for blood biomarker study by using global gene
expression profiling of peripheral whole blood |
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Ze Tian,
Nathan Palmer, Patrick Schmid, H. Yao, Michal Galdzicki,
Bonnie Berger*, Erxi Wu* and Isaac S. Kohane
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PLoS One 2009; 4 (4):e5157.Epub 2009 April 17
PMID 19381341 (PubMed - in process) |
Comprehensive
dissection of PDGF-PDGFR signaling pathways in PDGFR genetically
defined cells |
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Erxi Wu, Nathan Palmer, Ze Tian, Annie P.
Moseman, Michal Galdzicki, Xuetao Wang, Bonnie Berger,
Hongbing Zhang and Isaac S. Kohane*
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PLoS ONE Computational
Biology 3 (11):
e3794.
http://dx.doi.org/doi:10.1371/journal.pone.0003794 |
IsoRankN: spectral methods for global alignment of multiple
protein networks |
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Chung-Shou Liao, Kanghao Lu, Michael Baym, Rohit Singh and
Bonnie Berger* |
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Bioinformatics 2009 25: i253 - i258. |
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2008 Publications
Revealing the spatial distribution of a disease while
preserving privacy |
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Shannon Wieland, Christopher Cassa, Kenneth Mandl* and Bonnie Berger* |
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Proceedings of the National Academy of Sciences (2008) 105:46, 17608-17613. |
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IsoRank:
Global alignment of multiple protein interaction networks with
applications to functional orthology detection |
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Rohit Singh, Jinbo Xu and Bonnie Berger* |
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Proceedings of the National Academy of Sciences (2008) 105:35, 12763-12768. |
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http://www.pnas.org/content/105/35/12763.full |
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High-resolution modeling of cellular signaling networks |
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Michael Baym, Chris Bakal, Norbert Perrimon and Bonnie Berger* |
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Proceedings of the 12th Annual International Conference on Research in Computational Molecular Biology (2008) LNBI 4955, 257-271 |
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http://dx.doi.org/10.1007/978-3-540-78839-3_22 |
Inverting the
viterbi algorithm: An abstract framework for structure design |
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Michael Schnall-Levin, Leonid Chindelevitch and Bonnie Berger* |
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Proceedings of the 25th International Conference on Machine Learning (2008). |
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http://portal.acm.org/citation.cfm?id=1390270 |
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2007 Publications |
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