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Highlighted Publications -
All Publications
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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 |
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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 |
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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 |
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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 |
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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 |
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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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| 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, Isaac S. Kohane
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PLoS ONE Computational
Biology 3(11):
e3794.
http://dx.doi.org/doi:10.1371/journal.pone.0003794 |
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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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| 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 |
| Influence Flow: Integrating
pathway-specific RNAi
data and protein interaction data |
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Rohit Singh and Bonnie Berger |
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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. |
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| abstract |
bibTeX citation |
publisher's site |
| Pairwise
global alignment of protein interaction networks by matching
neighborhood topology |
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Rohit Singh, Jinbo Xu and Bonnie Berger |
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Proceedings of the 11th Annual International Conference on Research
in Computational Molecular Biology (2007): Lecture Notes in Computer
Science 4453, 16-31. |
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abstract |
bibTeX citation |
publisher's site |
| Probabilistic
modeling of systematic errors in two-hybrid experiments |
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| David Sontag, Rohit Singh and Bonnie Berger |
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| Pacific Symposium on Biocomputing
(2007) 12, 445-457. |
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| abstract |
bibTeX citation |
bibTeX citation |
| Struct2Net: Integrating
structure into protein-protein interaction prediction |
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Rohit Singh, Jinbo Xu, and Bonnie Berger |
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In Proceedings of the 11th Pacific Symposium on Biocomputing (2006) 403-414. |
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abstract |
bibTeX citation |
Publisher's Site
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| Herpesviral
protein networks and their interaction with the human
proteome |
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Peter Uetz, Yu-An Dong, Christine Zeretzke, Christine Atzler, Armin Baiker,
Bonnie Berger, Seesandra Rajagopala, Maria Roupelieva, Dietlind Rose, Even Fossum
and Jürgen Haas |
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Science (2006), 13 January, 311, 239-242; published online 7 December 2005 [DOI: 10.1126/science.1116804] (in Reports). |
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abstract |
bibTeX citation |
Publisher's Site |
| Active
learning for sampling in time-series experiments: with
applications to gene expression analysis |
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Rohit Singh, Nathan Palmer, David Gifford, Bonnie Berger, and Ziv
Bar-Joseph |
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Proceedings of the 22nd Annual International Conference on Machine
Learning (2005) 833-840. |
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abstract |
bibTeX citation |
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