Bonnie Berger

According to our database1, Bonnie Berger authored at least 126 papers between 1990 and 2020.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of two.

Awards

ACM Fellow

ACM Fellow 2003, "For contributions to Computational Molecular Biology.".

Timeline

Legend:

Book 
In proceedings 
Article 
PhD thesis 
Other 

Links

Homepages:

On csauthors.net:

Bibliography

2020
A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets.
Proceedings of the Research in Computational Molecular Biology, 2020

Privacy-Preserving Biomedical Database Queries with Optimal Privacy-Utility Trade-Offs.
Proceedings of the Research in Computational Molecular Biology, 2020

Reconstructing continuous distributions of 3D protein structure from cryo-EM images.
Proceedings of the 8th International Conference on Learning Representations, 2020

2019
Seq: a high-performance language for bioinformatics.
Proc. ACM Program. Lang., 2019

Reconstructing continuously heterogeneous structures from single particle cryo-EM with deep generative models.
CoRR, 2019

Metagenomic binning through low-density hashing.
Bioinform., 2019

Geometric Sketching of Single-Cell Data Preserves Transcriptional Structure.
Proceedings of the Research in Computational Molecular Biology, 2019

Protecting Genomic Data Privacy with Probabilistic Modeling.
Proceedings of the Biocomputing 2019: Proceedings of the Pacific Symposium, 2019

Explicitly disentangling image content from translation and rotation with spatial-VAE.
Proceedings of the Advances in Neural Information Processing Systems 32: Annual Conference on Neural Information Processing Systems 2019, 2019

Learning protein sequence embeddings using information from structure.
Proceedings of the 7th International Conference on Learning Representations, 2019

Large-Margin Classification in Hyperbolic Space.
Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics, 2019

2018
Joker de Bruijn: Covering k-Mers Using Joker Characters.
J. Comput. Biol., 2018

Fast characterization of segmental duplications in genome assemblies.
Bioinform., 2018

A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models.
Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018

Latent Variable Model for Aligning Barcoded Short-Reads Improves Downstream Analyses.
Proceedings of the Research in Computational Molecular Biology, 2018

Generalizable Visualization of Mega-Scale Single-Cell Data.
Proceedings of the Research in Computational Molecular Biology, 2018

Positive-Unlabeled Convolutional Neural Networks for Particle Picking in Cryo-electron Micrographs.
Proceedings of the Research in Computational Molecular Biology, 2018

2017
2017 ISCB Innovator Award: Aviv Regev.
PLoS Computational Biology, 2017

2017 ISCB Overton Prize awarded to Christoph Bock.
PLoS Computational Biology, 2017

2017 Outstanding Contributions to ISCB Award: Fran Lewitter.
PLoS Computational Biology, 2017

2017 ISCB Accomplishment by a Senior Scientist Award given to Pavel Pevzner.
PLoS Computational Biology, 2017

Identification of protein complexes by integrating multiple alignment of protein interaction networks.
Bioinform., 2017

Message from the ISCB: 2017 Outstanding Contributions to ISCB Award Given to Fran Lewitter.
Bioinform., 2017

Message from the ISCB: 2017 ISCB Overton Prize Awarded to Christoph Bock.
Bioinform., 2017

Message from the ISCB: 2017 ISCB Accomplishment by a Senior Scientist Award Given to Pavel Pevzner.
Bioinform., 2017

Message from the ISCB: 2017 ISCB Innovator Award Given to Aviv Regev.
Bioinform., 2017

ISCB's initial reaction to New England Journal of Medicine editorial on data sharing.
Bioinform., 2017

Joker de Bruijn: Sequence Libraries to Cover All k-mers Using Joker Characters.
Proceedings of the Research in Computational Molecular Biology, 2017

2016
ISCB's Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing.
PLoS Computational Biology, 2016

Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers.
J. Comput. Biol., 2016

Computational biology in the 21st century: scaling with compressive algorithms.
Commun. ACM, 2016

Realizing privacy preserving genome-wide association studies.
Bioinform., 2016

Fast genotyping of known SNPs through approximate k-mer matching.
Bioinform., 2016

RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data.
Bioinform., 2016

Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning.
Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

Enabling Privacy Preserving GWAS in Heterogeneous Human Populations.
Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values.
Proceedings of the 2016 Data Compression Conference, 2016

2015
ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus.
PLoS Computational Biology, 2015

Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data.
J. Comput. Biol., 2015

Entropy-scaling search of massive biological data.
CoRR, 2015

Exploiting ontology graph for predicting sparsely annotated gene function.
Bioinform., 2015

Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus.
Bioinform., 2015

Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers.
Proceedings of the Algorithms in Bioinformatics - 15th International Workshop, 2015

One Size Doesn't Fit All: Measuring Individual Privacy in Aggregate Genomic Data.
Proceedings of the 2015 IEEE Symposium on Security and Privacy Workshops, 2015

Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks.
Proceedings of the Research in Computational Molecular Biology, 2015

HapTree-X: An Integrative Bayesian Framework for Haplotype Reconstruction from Transcriptome and Genome Sequencing Data.
Proceedings of the Research in Computational Molecular Biology, 2015

2014
HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data.
PLoS Computational Biology, 2014

Simultaneous Alignment and Folding of Protein Sequences.
J. Comput. Biol., 2014

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.
BMC Syst. Biol., 2014

Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification.
Proceedings of the Research in Computational Molecular Biology, 2014

2013
A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis.
BMC Bioinform., 2013

Reconstruction of phyletic trees by global alignment of multiple metabolic networks.
BMC Bioinform., 2013

Compressive genomics for protein databases.
Bioinform., 2013

Optimizing a global alignment of protein interaction networks.
Bioinform., 2013

2012
Making sense out of massive data by going beyond differential expression.
Proc. Natl. Acad. Sci. USA, 2012

Assessing statistical significance in causal graphs.
BMC Bioinform., 2012

SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone.
Bioinform., 2012

Editorial.
Bioinform., 2012

Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAs.
Proceedings of the Research in Computational Molecular Biology, 2012

2011
IsoBase: a database of functionally related proteins across PPI networks.
Nucleic Acids Res., 2011

Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models.
J. Comput. Biol., 2011

Preface: 14th International Conference on Research in Computational Molecular Biology (RECOMB 2010).
J. Comput. Biol., 2011

An Integrative Approach to Ortholog Prediction for Disease-Focused and Other Functional Studies.
BMC Bioinform., 2011

A method for probing the mutational landscape of amyloid structure.
Bioinformatics [ISMB/ECCB], 2011

Sparse estimation for structural variability.
Algorithms Mol. Biol., 2011

Metabolic Network Analysis Demystified.
Proceedings of the Research in Computational Molecular Biology, 2011

2010
Markov random fields reveal an N-terminal double beta-propeller motif as part of a bacterial hybrid two-component sensor system.
Proc. Natl. Acad. Sci. USA, 2010

Struct2Net: a web service to predict protein-protein interactions using a structure-based approach.
Nucleic Acids Res., 2010

Local Optimization for Global Alignment of Protein Interaction Networks.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

2009
BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis.
PLoS Computational Biology, 2009

RNAmutants: a web server to explore the mutational landscape of RNA secondary structures.
Nucleic Acids Res., 2009

IsoRankN: spectral methods for global alignment of multiple protein networks.
Bioinform., 2009

2008
Global alignment of multiple protein interaction networks with application to functional orthology detection.
Proc. Natl. Acad. Sci. USA, 2008

Efficient Algorithms for Probing the RNA Mutation Landscape.
PLoS Computational Biology, 2008

Matt: Local Flexibility Aids Protein Multiple Structure Alignment.
PLoS Computational Biology, 2008

Optimal contact map alignment of protein-protein interfaces.
Bioinform., 2008

Graph algorithms for biological systems analysis.
Proceedings of the Nineteenth Annual ACM-SIAM Symposium on Discrete Algorithms, 2008

High-Resolution Modeling of Cellular Signaling Networks.
Proceedings of the Research in Computational Molecular Biology, 2008

Global Alignment of Multiple Protein Interaction Networks.
Proceedings of the Biocomputing 2008, 2008

Inverting the Viterbi algorithm: an abstract framework for structure design.
Proceedings of the Machine Learning, 2008

2007
Automated real time constant-specificity surveillance for disease outbreaks.
BMC Med. Inf. & Decision Making, 2007

A Parameterized Algorithm for Protein Structure Alignment.
J. Comput. Biol., 2007

Predicting and Annotating Catalytic Residues: An Information Theoretic Approach.
J. Comput. Biol., 2007

Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology.
Proceedings of the Research in Computational Molecular Biology, 2007

Probabilistic Modeling of Systematic Errors in Two-Hybrid Experiments.
Proceedings of the Biocomputing 2007, 2007

Lthreader: Prediction of Ligand-Receptor Interactions Using Localized Threading.
Proceedings of the Biocomputing 2007, 2007

2006
transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels.
Nucleic Acids Res., 2006

Fast and accurate algorithms for protein side-chain packing.
J. ACM, 2006

Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction.
Proceedings of the Biocomputing 2006, 2006

2005
Wrap-and-Pack: A New Paradigm for Beta Structural Motif Recognition with Application to Recognizing Beta Trefoils.
J. Comput. Biol., 2005

ChainTweak: Sampling from the Neighbourhood of a Protein Conformation.
Proceedings of the Biocomputing 2005, 2005

Active learning for sampling in time-series experiments with application to gene expression analysis.
Proceedings of the Machine Learning, 2005

A Tree-Decomposition Approach to Protein Structure Prediction.
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005

2004
msari.
Proc. Natl. Acad. Sci. USA, 2004

Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery.
J. Comput. Biol., 2004

Wrap-and-pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils.
Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, 2004

2003
Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species.
Proceedings of the Sventh Annual International Conference on Computational Biology, 2003

2002
Predicting the Beta-Helix Fold from Protein Sequence Data.
J. Comput. Biol., 2002

Trilogy: discovery of sequence-structure patterns across diverse proteins.
Proceedings of the Sixth Annual International Conference on Computational Biology, 2002

2000
Local rule mechanism for selecting icosahedral shell geometry.
Discret. Appl. Math., 2000

Human and mouse gene structure: comparative analysis and application to exon prediction.
Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000

Sequencing a genome by walking with clone-end sequences: a mathematical analysis (abstract).
Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000

1999
A Dictionary-Based Approach for Gene Annotation.
J. Comput. Biol., 1999

On the Structure of the Scaffolding Core of Bacteriophage T4.
J. Comput. Biol., 1999

Reconstructing a Three-Dimensional Model with Arbitrary Errors.
J. ACM, 1999

A dictionary based approach for gene annotation.
Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology, 1999

1998
Near-Linear Time Construction of Sparse Neighborhood Covers.
SIAM J. Comput., 1998

Computational learning reveals coiled coil-like motifs in histidine kinase linker domains.
Proc. Natl. Acad. Sci. USA, 1998

Protein Folding in the Hydrophobic-Hydrophilic(HP) Model is NP-Complete.
J. Comput. Biol., 1998

Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete.
Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, 1998

1997
The Fourth Moment Method.
SIAM J. Comput., 1997

An Iterative Method for Improved Protein Structural Motif Recognition.
J. Comput. Biol., 1997

Tight Bounds for the Maximum Acyclic Subgraph Problem.
J. Algorithms, 1997

1996
Fast Distributed Network Decompositions and Covers.
J. Parallel Distributed Comput., 1996

1995
Algorithms for Protein Structural Motif Recognition.
J. Comput. Biol., 1995

Scheduling with Concurrency-Based Constraints.
J. Algorithms, 1995

Nearly Optimal Algorithms and Bounds for Multilayer Channel Routing.
J. ACM, 1995

Improved Algorithms for Protein Motif Recognition.
Proceedings of the Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, 1995

1994
Low-Diameter Graph Decomposition Is in NC.
Random Struct. Algorithms, 1994

Efficient NC Algorithms for Set Cover with Applications to Learning and Geometry.
J. Comput. Syst. Sci., 1994

1993
Near-Linear Cost Sequential and Distribured Constructions of Sparse Neighborhood Covers
Proceedings of the 34th Annual Symposium on Foundations of Computer Science, 1993

1992
Fast Network Decomposition (Extended Abstract).
Proceedings of the Eleventh Annual ACM Symposium on Principles of Distributed Computing, 1992

1991
Simulating (log c n)-Wise Independence in NC.
J. ACM, 1991

Complexity Results and Algorithms for { <, <=, = }-Constrained Scheduling.
Proceedings of the Second Annual ACM/SIGACT-SIAM Symposium on Discrete Algorithms, 1991

1990
A Better Performance Guarantee for Approximate Graph Coloring.
Algorithmica, 1990

Approximation Algorithms for the Maximum Acyclic Subgraph Problem.
Proceedings of the First Annual ACM-SIAM Symposium on Discrete Algorithms, 1990


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