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

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

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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.

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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.

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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.

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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.

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'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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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Local topology of silica networks

L.W. Hobbs, Esther Jesurum, Vinay Pulim and Bonnie Berger

Philosophical Magazine (1998) A 78, 679-711.

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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.

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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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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.

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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.

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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.

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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.

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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.

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An iterative method for improved protein structural motif recognition

Bonnie Berger and Mona Singh

Journal of Computational Biology (1997) 4 no. 3, 261-273.

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The fourth moment method

Bonnie Berger

SIAM Journal on Computing (1997) 26 no. 4, 1188-1207.

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Tight bounds for the maximum acyclic subgraph problem

Bonnie Berger and Peter W. Shor

Journal of Algorithms (1997) 25 no. 1, 1-18.

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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.

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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.

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1995 Publications

Algorithms for protein structural motif recognition

Bonnie Berger

Journal of Computational Biology (1995) 2 no. 1, 125-138.

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Scheduling with concurrency-based constraints

Bonnie Berger and Lenore Cowen

Journal of Algorithms (1995) 18 no. 1, 98-123.

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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.

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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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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.

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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.

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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.

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1991 Publications

Simulating (log^c n)-wise independence in NC

Bonnie Berger and John Rompel

Journal of the Association for Computing Machinery (1991) 38 no. 4, 1026-1046.

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1990 Publications

A better performance guarantee for approximate graph coloring

Bonnie Berger and John Rompel

Algorithmica (1990) 5 no. 3, 459-466.

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

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

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

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