Professor
Bonnie Berger

  Berger Publications

Selected Publications List (with brief descriptions) - All Publications

(* for corresponding author or for my student is first author)

2014 Publications

Quality Score Compression Improves Genotyping Accuracy

Yun William Yu, Deniz Yorukoglu, Jian Peng and Bonnie Berger
Nature Biotechnology, in press.

Ancient Human Genomes Suggest Three Ancestral Populations for Present-Day Europeans

Iosif Lazaridis, Nick Patterson, Alissa Mittnik, Gabriel Renaud, Swapan Mallick, Karola Kirsanow, Peter H. Sudmant, Joshua G. Schraiber, Sergi Castellano, Mark Lipson, Bonnie Berger, et al
Nature, in press.

Reconstructing Austronesian Population History in Island Southeast Asia

Mark Lipson, Po-Ru Loh, Nick Patterson, Priya Moorjani, Ying-Chin Ko, Mark Stoneking, Bonnie Berger and David Reich
Nature Communications (2014), http://www.biorxiv.org/content/early/2014/05/27/005603, preprint.

Improving Power in GWAS while Addressing Confounding from Population Stratification with PC-Select

George Tucker, Alkes L. Price and Bonnie Berger *
Genetics, in press.

HapTree: A novel Bayesian Framework for Single Individual Polyplotyping using NGS Data
Emily Berger, Deniz Yorukoglu, Jian Peng and Bonnie Berger
PLOS Computational Biology Published: March 27, 2014 DOI: 10.1371/journal.pcbi.1003502, also accepted for presentation RECOMB 2014.

A Quantitative Chaperone Interaction Network Reveals the Architecture of Cellular Protein Homeostasis Pathways

Mikko Taipale, George Tucker, Jian Peng, Irina Krykbaeva, Zhen-Yuan Lin, Brett Larsen, Hyungwon Choi, Bonnie Berger, Anne-Claude Gingras *, and Susan Lindquist *
Cell, in press.

Network Topology and Parameter Estimation: From Experimental Design Methods to Gene Regulatory Network Kinetics using a Community Based Approach
Pablo Meyer, Thomas Cokelaer, Deepak Chandran, Kyung Hyuk Kim, Po-Ru Loh, George Tucker, Mark Lipson, Bonnie Berger, Clemens Kreutz, Andreas Raue, Bernhard Steiert, Jens Timmer, Erhan Bilal, DREAM 6&7 Parameter Estimation consortium, Herbert M Sauro, Gustavo Stolovitzky, and Julio Saez-Rodriguez
BMC Systems Biology 2014, 8:13   http://www.biomedcentral.com/1752-0509/8/13#sec8

Simultaneous Alignment and Folding of Protein Sequences
Jerome Waldispuhl, Rolf Backofen, Charles W. O'Donnell, Sebastian Will, Srini Devadas and Bonnie Berger
Journal of Computational Biology, in press.

Ancient West Eurasian Ancestry in Southern and Eastern Africa
Joseph K. Pickrell, Nick Patterson, Po-Ru Loh, Mark Lipson, Bonnie Berger, Mark Stoneking, Brigitte Pakendorf and David Reich.
Proceedings of the National Academy of Sciences, 111, 7 (2014): 2632-2637 http://www.pnas.org/citmgr?gca=pnas;111/7/2632

2013 Publications

Computational Solutions for "Omics Data"
Bonnie Berger, Jian Peng and Mona Singh
Nature Reviews Genetics, 14 (2013): 333-346 http://www.nature.com/nrg/journal/v14/n5/abs/nrg3433.html

HapTree: A novel Bayesian Framework for Single Individual Polyplotyping using NGS Data
Emily Berger, Deniz Yorukoglu, Jian Peng and Bonnie Berger
PLOS Computational Biology Published: March 27, 2014 DOI: 10.1371/journal.pcbi.1003502, also accepted for presentation RECOMB 2014.

A sampling framework for incorporating quantitative mass spectrometry data in protein interaction
George Tucker, Po-Ru Loh and Bonnie Berger
BMC Bioinformatics 2013, 14:299 http://www.biomedcentral.com/1471-2105/14/299/

Traversing the K-mer Landscape of NGS Read Datasets for Quality Score Sparsification
Y. William Yu, Deniz Yorukoglu and Bonnie Berger
Accepted presentation for RECOMB 2014 http://link.springer.com/chapter/10.1007/978-3-319-05269-4_31

Compressive Genomics for Protein Databases
Noah Daniels, Andrew Gallant, Jian Peng, Michael Baym, Lenore Cowen and Bonnie Berger *
Bioinformatics 29, 13 (2013): i283-i290 http://bioinformatics.oxfordjournals.org/content/29/13/i283.abstract

Optimizing a Global Alignment of Protein Interaction Networks
Leonid Chindelevitch, Cheng-Yu Ma, Chung-Shou Liao and Bonnie Berger *
Bioinformatics, published online September 17, 2013 http://bioinformatics.oxfordjournals.org/content/early/2013/09/17/bioinformatics.btt486.short

Genetic Determinants of Phosphate Response in Drosophlia
Clemens Bergwitz *, Mark J. Wee, Sumi Sinha, Joanne Huang, Charles DeRobertis, Lawrence B. Mensah, Jonathan Cohen, Adam Friedman, Meghana Kulkarni, Yanhui Hu, Arunachanlam Vinayagam, Michael Schnall-Levin, Bonnie Berger, Lizabeth A. Perkins, Stephanie E. Mohr and Norbert Perrimon.
PLoS ONE 8, 3 (2013): e56753 http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056753

Genetic Evidence for Recent Population Mixture in India
Priya Moorjani *, Kumarasamy Thangaraj *, Nick Patterson, Mark Lipson, Po-Ru Loh, Periyasamy Govindaraj, Bonnie Berger, David Reich and Lalji Singh.
The American Journal of Human Genetics, 93,5 (2013):422-438

Efficient Moment-based Inference of Admixture Parameters and Sources of Gene Flow
Mark Lipson, Po-Ru Loh, Alex Levin, David Reich, Nick Patterson and Bonnie Berger *
Molecular Biology and Evolution, published online: May 24, 2013. http://mbe.oxfordjournals.org/content/early/2013/05/24/molbev.mst099.abstract?keytype=ref&ijkey=L24bMzDMQIziRkq

Reconstruction of Phyletic Trees by Global Alignment of Multiple Metabolic Networks
Cheng-Yu Ma, Shu-Hsi Lin, Chi-Ching Lee, Chuan Yi Tang, Bonnie Berger and Chung-Shou Liao
BMC Bioinformatics, 14 (2013) Suppl 2:S12 http://www.biomedcentral.com/1471-2105/14/S2/S12#

Reconstructing Roma History from Genome-Wide Data
Priya Moorjani, Nick Patterson, Po-Ru Loh, Mark Lipson, Peter Kisfali, Bela I. Melegh, Michael Bonin, L'udevit Kadasi, Olaf Rieb, Bonnie Berger *, David Reich *, and Bela Melegh
PLoS One 8 3 (2013): e58633 http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058633

Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium
Po-Ru Loh , Mark Lipson, Nick Patterson, Priya Moorjani, Joseph K. Pickrell, David Reich * and Bonnie Berger *
Genetics Mon. 1 Apr 2013 13:03:15 -0400,  http://www.genetics.org/content/193/4.cover-expansion

Structure-based Whole Genome Realignment Reveals Many Novel Non-coding RNAs
Sebastian Will, Michael Yu and Bonnie Berger *
Genome Research 23 6 (2013): 1018-1027 http://link.springer.com/chapter/10.1007/978-3-642-29627-7_35, also appeared in RECOMB 2012.

2012 Publications

Compressive Genomics
Po-Ru Loh, Michael Baym and Bonnie Berger *
Nature Biotechnology 30 (2012) 627-630 Published online 10 July 2012 http://www.nature.com/nbt/journal/v30/n7/full/nbt.2241.html

Computational Analysis of Noncoding RNAs
Stefan Washietl, Sebastian Will , David A. Hendrix, Loyal A. Goff, John L. Rinn, Bonnie Berger, and Manolis Kellis
WIREs RNA 3 (2012):759-778 http://wires.wiley.com/WileyCDA/WiresArticle/wisId-WRNA1134.html

The Genetic Prehistory of Southern Africa
Joseph K. Pickrell, Nick Patterson, Chiara Barbieri, Falko Berthold, Linda Gerlach, Tom Güldemann, Blesswell Kure, Sununguko Wata Mpoloka, Hirosi Nakagawa, Christfried Naumann, Mark Lipson, Po-Ru Loh, Joseph Lachance, Joanna Mountain, Carlos Bustamante, Bonnie Berger, SarahTishkoff, Brenna Henn, Mark Stoneking, David Reich, and Brigitte Pakendorf
Nature Communications 16 (2012)3:1143 http://www.ncbi.nlm.nih.gov/pubmed/23072811


A computational framework for boosting confidence in high-throughput protein-protein interaction datasets
Raghavendra Hosur, Jian Peng, Arunachalam Vinayagam, Ulrich Stelzl, Jinbo Xu, Norbert Perrimon, Jadwiga Bienkowska, and Bonnie Berger *
Genome Biology 13 (2012) R76  http://genomebiology.com/content/pdf/gb-2012-13-8-r76.pdf

A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers
Nathan Palmer, Patrick Schmid, Bonnie Berger * and Isaac Kohane
Genome Biology 13 (2012) 8:R71  http://genomebiology.com/2012/13/8/R71

SMURFLite: combining simplified markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone
Noah M. Daniels, Raghavendra Hosur, Bonnie Berger * and Lenore Cowen *
Bioinformatics 28 (2012) 9:1216-1222 http://bioinformatics.oxfordjournals.org/content/28/9/1216.full

Making sense out of massive data by going beyond differential gene expression
Patrick Schmid, Nathan Palmer, Isaac Kohane and Bonnie Berger *
Proceedings of the National Academy of Sciences 109 (2012) no. 15:5549-5906 http://www.pnas.org/content/early/2012/03/21/1118792109

Assessing statistical significance in causal graphs
Leonid Chindelevich, Po-Ru Loh, Ahmed Enayetallah, Bonnie Berger and Daniel Ziemek *
BMC Bioinformatics 13 (2012) no.35 http://www.biomedcentral.com/1471-2105/13/35

MetaMerge: Scaling up genome-scale metabolic reconstructions with application to mycobacterium tuberculosis
Leonid Chindelevich , Sarah Stanley, Deborah Hung, Aviv Regev and Bonnie Berger *
Genome Biology 13 (2012) r6 http://genomebiology.com/2012/13/1/r6

STITCHER: Dynamic assembly of likely amyloid and prion beta-structures from secondary structure predictions
Allen W. Bryan, Jr., Charles W. O'Donnell, Matthew Menke, Lenore Cowen, Susan Lindquist and Bonnie Berger * http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3298606/
PROTEINS: Structure, Function Bioinformatics (2012) 80 no. 2
 
Structure-based whole genome realignment reveals many novel non-coding RNA's
Sebastian Will, Michael Yu and Bonnie Berger
Proc 16th Annual International Conference on Research in Molecular Biology, LNCS (2012) Abstract only

2011 Publications

Genomics in 2011: challenges and opportunities
Davis Adams, Bonnie Berger, Olivier Harismendy, Curtis Huttenhower, X Shirley Liu, Chad Myers, Alicia Oshlack, John Rinn and Marian Walhout
Genome Biology 12 (2011):137. http://genomebiology.com/2011/12/12/137

An integrative approach to ortholog prediction for disease-focused and other functional studies
Yanhui Hu, Ian Flockhart, Arunachalam Vinayagam, Clemens Bergwitz, Bonnie Berger, Norbert Perrimon and Stephanie E. Mohr.
BCM Bioinformatics (2011) 12 357 http://www.biomedcentral.com/1471-2105/12/357

Building quantitative prediction models for tissue residue of two explosives compounds in earthworms from microarray gene expression data
Ping Gong, Po-Ru Loh, Natalie Barker, George Tucker, Nan Wang, Chen Jua Zhang, B. Lynn Escalon, Bonnie Berger and Edward Perkins
Environmental Science and Technology (2011) Aug 8. Epub ahead of print. http://www.ncbi.nlm.nih.gov/pubmed/21776976

Multicoil2: Predicting coiled coils and their oligomerization states from sequence in the twilight zone
Jason Trigg, Karl Gutwin, Amy E. Keating* and Bonnie Berger*
PLoS ONE (2011) 6 8:e23519 doi:10.1371/journal.pone.0023519

Unusually effective microRNA targeting within repeat-rich coding regions of mamalian mRNAs
Michael Schnall-Levin , Olivia Rissland, Wendy Johnston, Norbert Perrimon, David Bartel* and Bonnie Berger*
Genome Research (2011) http://genome.cshlp.org/content/early/2011/06/16/gr.121210.111?top=1
   
Proteomic and functional genomic landscape of receptor tyrosine kinase and Ras/ERK signaling
A. A. Friedman, G. Tucker, R. Singh, D. Yan,  A. Vimayagam, Y. Hu, R. Binari, P. Hong, X. Sun, M. Porto, S. Pacifico, T. Murali, R. L. Finley, Jr., J. M. Asara, B. Berger and N. Perrimon.
Science Signaling 4, no. 196 (2011): p.rs 10 DOI:10.1126/scisignal.2002029
 
A method for probing the mutational landscape of amyloid structure.
Charles W. O'Donnell , Jerome Waldispühl, 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. Bioinformatics (2011) 27 13: i34-i42 doi.org/10.1093/bioinformatics/btr238
 
Structure-based prediction reveals capping motifs that inhibit β-helix aggregation.
Allen W. Bryan, Jr. , Jennifer Starner-Kreinbrink, Raghavendra Hosur, Patricia Clark* and Bonnie Berger*
Proceedings of the National Academy of Sciences (2011) 108, 27: 11099-11104
doi: 10.1073/pnas.1017504108

Opposing effects of glutamine and asparagine govern prion formation by intrinsically disordered proteins.
Randal Halfmann, Simon Alberti, Rajaraman Krishnan, Nicholas Lyle, Charles W. O'Donnell, Oliver D. King, Bonnie Berger, Rohit V. Pappu and Susan Lindquist*
Molecular Cell (2011) 43, 1:72-84 doi.org/10.1016/j.molcel.2011.05.013

Efficient traversal of protein folding pathways using ensemble models
Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger* and Jerome Waldispühl*
Lecture Notes in Computer Science (2011) Vol. 6577, 408-423 doi:10.1007/978-3-642-20036-6_38

IsoBase: a database of functionally related proteins across PPI Networks
Daniel Park , Rohit Singh, Michael Baym, Chung-Shou Liao and Bonnie Berger*
Nucleic Acids Research (2011) 39, (suppl 1): D295-D300  http://nar.oxfordjournals.org/content/39/suppl_1/D295.abstract

Metabolic network analysis demystified
Leoind Chindelevich, Aviv Regev and Bonnie Berger*
Lecture Notes in Computer Science (2011) Vol. 6577 ISBN 978-3-642-20035-9 Springer Berlin Heidelberg, p. 31 (Abstract only). doi:10.1007/978-3-642-20036-6_3

2010 Publications

Identification of functional elements and regulatory circuits by drosophila modENCODE
The ModEncode Consortium
Science (2010) 330:6012, 1787-1797 DOI: 10.1126/science.1198374

Conserved microRNA targeting in drosophila is as widespread in coding regions as in 3' UTRs
Michael Schnall-Levin, Yong Zhao, Norbert Perrimon* and Bonnie Berger*
Proceedings of the National Academy of Sciences (2010) 107:36, 15751-15756

Phenotype prediction in DREAM5 via regression variants
Po-Ru Loh †, George Tucker, Michael Yu and Bonnie Berger*
Winner, DREAM5 Challenge 3B Competition. Presented at RECOMB 2010 Systems Biology Satellite Conference

Sparse estimation for structural variability
Raghavendra Hosur, Rohit Singh and Bonnie Berger*
Algorithms for Molecular Biology (2011) 6:12 Selected for fast-track publication in AMB from WABI 2010.

Struct2Net: A web service to predict protein-protein interactions using a structure-based approach
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

iWRAP: An interface threading approach with application to prediction of cancer related protein-protein interactions
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

Inference of RhoGAP/GTPase regulation using single-cell morphological data from a combinatorial RNAiScreen
Oaz Nir , Chris Bakal, Norbert Perrimon and Bonnie Berger*
Genome Research (2010) 20: 372-380 doi:10.1101/gr.101246.109

Local optimization for the global alignment of protein interaction networks
Leonid Chindelevitch , Chung-Shou Liao and Bonnie Berger*
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
Matt Menke , Bonnie Berger* and Lenore Cowen*
Proceedings of the National Academy of Sciences (2010) www.pnas.org/cgi/doi/10.1073/pnas.0909950107

2009 Publications

Matt: Local flexibility aids protein multiple structure alignment
Matt Menke, Bonnie Berger*, Lenore Cowen*
PloS Computational Biology, 4 Issue 1 http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0040010

Large-scale identification of genetic design strategies using local search
Desmond S. Lun, Graham Rockwell, Nicholas J. Guido, Michael Baym, Jonathan A. Kelner, Bonnie Berger, James E. Galagan and George M. Church*
Nature Molecular Systems Biology http://www.nature.com/msb/journal/v5/n1/full/msb200957.html

RNAiCut: automated detection of significant genes from functional genomic screens
Irene Kaplow , Rohit Singh, Adam Friedman, Chris Bakal, Norbert Perrimon* and Bonnie Berger*
Nature Methods (2009) 6 (7):476-7 http://www.nature.com/nmeth/journal/v6/n7/full/nmeth0709-476.html

RNAmutants: a web server to explore the mutational landscape of RNA secondary structures
Jerome Waldispühl, Srinivas Devadas, Bonnie Berger* and Peter Clote*
Nucleic Acids Research (2009) 37:46, W281-W286
 
Vectorial Transport and Folding of an Autotransporter Virulence Protein during Outer Membrane Secretion
Mirco Junker, Andrew McDonnell, Bonnie Berger, Ti Li, Ning Zheng and Patricia Clark

Biophysical Journal (2009) 96 issue 3 http://dx.doi.org/10.1016/j.bpj.2008.12.1677


Simultaneous alignment and folding of protein sequences
Jerome Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen and Bonnie Berger*

Lecture Notes in Computer Science, Research in Computational Molecular Biology, Vol. 5541/2009, p. 339-355, 2009. http://dx.doi.org/10.1007/978-3-642-02008-7_25


BETASCAN: Probable β-amyloids identified by pairwise probabilistic analysis

Allen W. Bryan, Jr, Matthew Menke, Lenore J. Cowen, Susan L. Lindquist* and Bonnie Berger*

PLoS Computational Biology  5(3): e1000333.

http://dx.doi.org/doi:10.1371/journal.pcbi.1000333

http://betascan.csail.mit.edu

 

A practical platform for blood biomarker study by using global gene expression profiling of peripheral whole blood

Ze Tian, Nathan Palmer, Patrick Schmid, H. Yao, Michal Galdzicki, Bonnie Berger*, Erxi Wu* and Isaac S. Kohane

PLoS One 2009; 4 (4) PMID 19381341

 

Comprehensive dissection of PDGF-PDGFR signaling pathways in PDGFR genetically defined cells

Erxi Wu, Nathan Palmer, Ze Tian, Annie P. Moseman, Michal Galdzicki, Xuetao Wang, Bonnie Berger, Hongbing Zhang and Isaac S. Kohane*

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 
Chung-Shou Liao, Kanghao Lu, Michael Baym, Rohit Singh and Bonnie Berger*
Bioinformatics 2009 25: i253 - i258.

2008 Publications

Revealing the spatial distribution of a disease while preserving privacy
Shannon Wieland, Christopher Cassa, Kenneth Mandl* and Bonnie Berger*
Proceedings of the National Academy of Sciences (2008) 105:46, 17608-17613.

IsoRank: Global alignment of multiple protein interaction networks with applications to functional orthology detection
Rohit Singh, Jinbo Xu and Bonnie Berger*
Proceedings of the National Academy of Sciences (2008) 105:35, 12763-12768.   
http://www.pnas.org/content/105/35/12763.full

Optimal contact map alignment of protein-protein interfaces
Vinay Pulim, Bonnie Berger* and Jadwiga Bienkowska*
Bioinformatics (Oxford, England) 24:20, 2324-2328.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/20/2324

 

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
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*
Proceedings of the 25th International Conference on Machine Learning (2008).
http://portal.acm.org/citation.cfm?id=1390270
 
Efficient algorithms for probing the RNA mutation landscape
Jerome Waldispühl, Srini Devadas, Bonnie Berger and Peter Clote*
PLoS Computational Biology 4, (8).
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000124
 
 
Lthreader: Prediction of extracellular ligand-receptor interactions in cytokines using localized threading
Vinay Pulim, Jadwiga Bienkowska and Bonnie Berger
Protein Science, 17: 1-14.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18096641

Global alignment of multiple protein interaction networks
Rohit Singh, Jinbo Xu and Bonnie Berger*
Proceedings 13th Pacific Symposium on Biocomputing (2008)13,303-314.
http://www.ncbi.nlm.nih.gov/pubmed/18229695

Matt: Local flexibility aids protein multiple structure alignment
Matt Menke, Bonnie Berger* and Lenore Cowen*
PLoS Computational Biology 4, Issue 1.
http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0040010
 
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, 1058-73.
 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

Probabilistic modeling of systematic errors in two-hybrid experiments
David Sontag, Rohit Singh and Bonnie Berger*
Pacific Symposium on Biocomputing (2007) 12, 445-457.
abstract  bibTeX citation   bibTeX citation

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.
doi:10.1002/prot.21788

 
2006 Publications
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) 22 (3), 356-358. doi: 10.1093/bioinformatics/bti797
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) 53:4, 533 -557.
abstract  bibTeX citation  
 
2005 Publications
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 neighborhood 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.
abstract  bibTeX citation  
 
2004 Publications
  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

 
2002 Publications
  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

 
2001 Publications
  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

 
2000 Publications
  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

 
1999 Publications
  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

 

 
1998 Publications
  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 topology of silica networks
  L.W. Hobbs, Esther Jesurum, Vinay Pulim and Bonnie Berger
  Philosophical Magazine (1998) A 78, 679-711.
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

 
1997 Publications
  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

  The fourth moment method
  Bonnie Berger
  SIAM Journal on Computing (1997) 26 no. 4, 1188-1207.
abstract  bibTeX citation publisher's site

  Tight bounds for the maximum acyclic subgraph problem
  Bonnie Berger and Peter W. Shor
  Journal of Algorithms (1997) 25 no. 1, 1-18.
abstract  bibTeX citation publisher's site

 
1996 Publications
  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  

 
1995 Publications
  Algorithms for protein structural motif recognition
  Bonnie Berger
  Journal of Computational Biology (1995) 2 no. 1, 125-138.
abstract  bibTeX citation  

  Scheduling with concurrency-based constraints
  Bonnie Berger and Lenore Cowen
  Journal of Algorithms (1995) 18 no. 1, 98-123.
abstract  bibTeX citation publisher's site

  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

 
1994 Publications
  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  

 
1991 Publications
  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  

 
1990 Publications
  A better performance guarantee for approximate graph coloring
  Bonnie Berger and John Rompel
  Algorithmica (1990) 5 no. 3, 459-466.
abstract  bibTeX citation  

colspan="5" bgcolor="#000000">