Bonnie Berger
Orcid: 0000-0002-2724-7228Affiliations:
- MIT, Cambridge, USA
According to our database1,
Bonnie Berger
authored at least 149 papers
between 1990 and 2024.
Collaborative distances:
Collaborative distances:
Awards
ACM Fellow
ACM Fellow 2003, "For contributions to Computational Molecular Biology.".
Timeline
Legend:
Book In proceedings Article PhD thesis Dataset OtherLinks
Online presence:
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on zbmath.org
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on orcid.org
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on id.loc.gov
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on dl.acm.org
On csauthors.net:
Bibliography
2024
2023
TT3D: Leveraging precomputed protein 3D sequence models to predict protein-protein interactions.
Bioinform., October, 2023
Nucleic Acids Res., July, 2023
virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2.
J. Comput. Biol., 2023
CoRR, 2023
Proceedings of the 44th IEEE Symposium on Security and Privacy, 2023
Proceedings of the 32nd ACM SIGPLAN International Conference on Compiler Construction, 2023
2022
CoRR, 2022
Sequre: a high-performance framework for rapid development of secure bioinformatics pipelines.
Proceedings of the IEEE International Parallel and Distributed Processing Symposium, 2022
Proceedings of the Tenth International Conference on Learning Representations, 2022
2021
IEEE Trans. Inf. Theory, 2021
Bayesian information sharing enhances detection of regulatory associations in rare cell types.
Bioinform., 2021
Multi-resolution modeling of a discrete stochastic process identifies causes of cancer.
Proceedings of the 9th International Conference on Learning Representations, 2021
CryoDRGN2: Ab initio neural reconstruction of 3D protein structures from real cryo-EM images.
Proceedings of the 2021 IEEE/CVF International Conference on Computer Vision, 2021
2020
Meta-analysis of Caenorhabditis elegans single-cell developmental data reveals multi-frequency oscillation in gene activation.
Bioinform., 2020
Bioinform., 2020
Bioinform., 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
Proceedings of the Advances in Neural Information Processing Systems 33: Annual Conference on Neural Information Processing Systems 2020, 2020
Proceedings of the 8th International Conference on Learning Representations, 2020
2019
Reconstructing continuously heterogeneous structures from single particle cryo-EM with deep generative models.
CoRR, 2019
Proceedings of the Research in Computational Molecular Biology, 2019
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
Proceedings of the 7th International Conference on Learning Representations, 2019
Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics, 2019
2018
J. Comput. Biol., 2018
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
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
PLoS Comput. Biol., 2017
F1000Research, 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
Bioinform., 2017
Message from the ISCB: 2017 ISCB Accomplishment by a Senior Scientist Award Given to Pavel Pevzner.
Bioinform., 2017
Bioinform., 2017
ISCB's initial reaction to New England Journal of Medicine editorial on data sharing.
Bioinform., 2017
Proceedings of the Research in Computational Molecular Biology, 2017
2016
ISCB's Initial Reaction to <i>The New England Journal of Medicine</i> Editorial on Data Sharing.
PLoS Comput. Biol., 2016
J. Comput. Biol., 2016
Commun. ACM, 2016
Bioinform., 2016
RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data.
Bioinform., 2016
Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016
Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016
Proceedings of the 2016 Data Compression Conference, 2016
2015
ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus.
PLoS Comput. Biol., 2015
J. Comput. Biol., 2015
Bioinform., 2015
Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus.
Bioinform., 2015
Proceedings of the Algorithms in Bioinformatics - 15th International Workshop, 2015
Proceedings of the 2015 IEEE Symposium on Security and Privacy Workshops, 2015
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 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
BMC Bioinform., 2013
2012
Proc. Natl. Acad. Sci. USA, 2012
SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone.
Bioinform., 2012
Proceedings of the Research in Computational Molecular Biology, 2012
2011
Nucleic Acids Res., 2011
J. Comput. Biol., 2011
Preface: 14<sup>th</sup> 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
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
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010
2009
PLoS Comput. Biol., 2009
RNAmutants: a web server to explore the mutational landscape of RNA secondary structures.
Nucleic Acids Res., 2009
Bioinform., 2009
2008
Global alignment of multiple protein interaction networks with application to functional orthology detection.
Proc. Natl. Acad. Sci. USA, 2008
PLoS Comput. Biol., 2008
PLoS Comput. Biol., 2008
Proceedings of the Nineteenth Annual ACM-SIAM Symposium on Discrete Algorithms, 2008
Proceedings of the Research in Computational Molecular Biology, 2008
Proceedings of the Biocomputing 2008, 2008
Proceedings of the Machine Learning, 2008
2007
BMC Medical Informatics Decis. Mak., 2007
J. Comput. Biol., 2007
Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology.
Proceedings of the Research in Computational Molecular Biology, 2007
Proceedings of the Biocomputing 2007, 2007
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
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
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
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005
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
Proceedings of the Sixth Annual International Conference on Computational Biology, 2002
2000
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
Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology, 1999
1998
Computational learning reveals coiled coil-like motifs in histidine kinase linker domains.
Proc. Natl. Acad. Sci. USA, 1998
J. Comput. Biol., 1998
Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, 1998
1997
J. Comput. Biol., 1997
1996
J. Parallel Distributed Comput., 1996
1995
Proceedings of the Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, 1995
1994
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
Proceedings of the Eleventh Annual ACM Symposium on Principles of Distributed Computing, 1992
1991
Proceedings of the Second Annual ACM/SIGACT-SIAM Symposium on Discrete Algorithms, 1991
1990
Proceedings of the First Annual ACM-SIAM Symposium on Discrete Algorithms, 1990