Bonnie Berger

ORCID

Publication Activity (10 Years)

Years Active: 1989-2024
Publications (10 Years): 71

Top Venues

Publications

Bowen Jing, Bonnie Berger, Tommi S. Jaakkola
AlphaFold Meets Flow Matching for Generating Protein Ensembles. CoRR (2024)
Matthew M. Hong, David Froelicher, Ricky Magner, Victoria Popic, Bonnie Berger, Hyunghoon Cho
Secure Discovery of Genetic Relatives Across Large-Scale and Distributed Genomic Datasets. RECOMB (2024)
Bowen Jing, Tommi S. Jaakkola, Bonnie Berger
Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms. ICLR (2024)
Hannes Stärk, Bowen Jing, Chenyu Wang, Gabriele Corso, Bonnie Berger, Regina Barzilay, Tommi S. Jaakkola
Dirichlet Flow Matching with Applications to DNA Sequence Design. CoRR (2024)
Sumaira Zaman, Samuel Sledzieski, Bonnie Berger, Yi-Chieh Wu, Mukul S. Bansal
virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2. J. Comput. Biol. 30 (1) (2023)
Samuel Sledzieski, Kapil Devkota, Rohit Singh, Lenore Cowen, Bonnie Berger
TT3D: Leveraging precomputed protein 3D sequence models to predict protein-protein interactions. Bioinform. 39 (10) (2023)
Bowen Jing, Ezra Erives, Peter Pao-Huang, Gabriele Corso, Bonnie Berger, Tommi S. Jaakkola
EigenFold: Generative Protein Structure Prediction with Diffusion Models. CoRR (2023)
David Froelicher, Hyunghoon Cho, Manaswitha Edupalli, Joao Sa Sousa, Jean-Philippe Bossuat, Apostolos Pyrgelis, Juan Ramón Troncoso-Pastoriza, Bonnie Berger, Jean-Pierre Hubaux
Scalable and Privacy-Preserving Federated Principal Component Analysis. SP (2023)
Simon Mendelsohn, David Froelicher, Denis Loginov, David Bernick, Bonnie Berger, Hyunghoon Cho
sfkit: a web-based toolkit for secure and federated genomic analysis. Nucleic Acids Res. 51 (W1) (2023)
Bowen Jing, Tommi S. Jaakkola, Bonnie Berger
Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms. CoRR (2023)
Alexander P. Wu, Thomas Markovich, Bonnie Berger, Nils Yannick Hammerla, Rohit Singh
Causally-guided Regularization of Graph Attention Improves Generalizability. Trans. Mach. Learn. Res. 2023 (2023)
David Froelicher, Hyunghoon Cho, Manaswitha Edupalli, Joao Sa Sousa, Jean-Philippe Bossuat, Apostolos Pyrgelis, Juan Ramón Troncoso-Pastoriza, Bonnie Berger, Jean-Pierre Hubaux
Scalable and Privacy-Preserving Federated Principal Component Analysis. CoRR (2023)
Ariya Shajii, Gabriel Ramirez, Haris Smajlovic, Jessica Ray, Bonnie Berger, Saman P. Amarasinghe, Ibrahim Numanagic
Codon: A Compiler for High-Performance Pythonic Applications and DSLs. CC (2023)
Alexander P. Wu, Thomas Markovich, Bonnie Berger, Nils Hammerla, Rohit Singh
Causally-guided Regularization of Graph Attention Improves Generalizability. CoRR (2022)
Rohit Singh, Alexander P. Wu, Bonnie Berger
Granger causal inference on DAGs identifies genomic loci regulating transcription. CoRR (2022)
Haris Smajlovic, Ariya Shajii, Bonnie Berger, Hyunghoon Cho, Ibrahim Numanagic
Sequre: a high-performance framework for rapid development of secure bioinformatics pipelines. IPDPS Workshops (2022)
Alexander P. Wu, Rohit Singh, Bonnie Berger
Granger causal inference on DAGs identifies genomic loci regulating transcription. ICLR (2022)
Ellen D. Zhong, Adam Lerer, Joseph H. Davis, Bonnie Berger
CryoDRGN2: Ab initio neural reconstruction of 3D protein structures from real cryo-EM images. ICCV (2021)
Adam Uri Yaari, Maxwell Sherman, Oliver Clarke Priebe, Po-Ru Loh, Boris Katz, Andrei Barbu, Bonnie Berger
Multi-resolution modeling of a discrete stochastic process identifies causes of cancer. ICLR (2021)
Alexander P. Wu, Jian Peng, Bonnie Berger, Hyunghoon Cho
Bayesian information sharing enhances detection of regulatory associations in rare cell types. Bioinform. 37 (Supplement) (2021)
Bonnie Berger, Michael S. Waterman, Yun William Yu
Levenshtein Distance, Sequence Comparison and Biological Database Search. IEEE Trans. Inf. Theory 67 (6) (2021)
Brian Hie, Ellen D. Zhong, Bryan Bryson, Bonnie Berger
Learning Mutational Semantics. NeurIPS (2020)
Luke A. D. Hutchison, Bonnie Berger, Isaac S. Kohane
Meta-analysis of Caenorhabditis elegans single-cell developmental data reveals multi-frequency oscillation in gene activation. Bioinform. 36 (13) (2020)
Benjamin Demeo, Bonnie Berger
Hopper: a mathematically optimal algorithm for sketching biological data. Bioinform. 36 (Supplement-1) (2020)
Ellen D. Zhong, Tristan Bepler, Joseph H. Davis, Bonnie Berger
Reconstructing continuous distributions of 3D protein structure from cryo-EM images. ICLR (2020)
Hyunghoon Cho, Sean Simmons, Ryan Kim, Bonnie Berger
Privacy-Preserving Biomedical Database Queries with Optimal Privacy-Utility Trade-Offs. RECOMB (2020)
Christopher Heje Grønbech, Maximillian Fornitz Vording, Pascal N. Timshel, Casper Kaae Sønderby, Tune H. Pers, Ole Winther, Bonnie Berger
scVAE: variational auto-encoders for single-cell gene expression data. Bioinform. 36 (16) (2020)
Baris Ekim, Bonnie Berger, Yaron Orenstein
A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets. RECOMB (2020)
Ellen D. Zhong, Tristan Bepler, Joseph H. Davis, Bonnie Berger
Reconstructing continuously heterogeneous structures from single particle cryo-EM with deep generative models. CoRR (2019)
Brian Hie, Hyunghoon Cho, Benjamin Demeo, Bryan Bryson, Bonnie Berger
Geometric Sketching of Single-Cell Data Preserves Transcriptional Structure. RECOMB (2019)
Tristan Bepler, Bonnie Berger
Learning protein sequence embeddings using information from structure. CoRR (2019)
Tristan Bepler, Ellen D. Zhong, Kotaro Kelley, Edward Brignole, Bonnie Berger
Explicitly disentangling image content from translation and rotation with spatial-VAE. NeurIPS (2019)
Sean Simmons, Bonnie Berger, Cenk S. Sahinalp
Protecting Genomic Data Privacy with Probabilistic Modeling. PSB (2019)
Tristan Bepler, Ellen D. Zhong, Kotaro Kelley, Edward Brignole, Bonnie Berger
Explicitly disentangling image content from translation and rotation with spatial-VAE. CoRR (2019)
Yunan Luo, Yun William Yu, Jianyang Zeng, Bonnie Berger, Jian Peng
Metagenomic binning through low-density hashing. Bioinform. 35 (2) (2019)
Hyunghoon Cho, Benjamin Demeo, Jian Peng, Bonnie Berger
Large-Margin Classification in Hyperbolic Space. AISTATS (2019)
Ariya Shajii, Ibrahim Numanagic, Riyadh Baghdadi, Bonnie Berger, Saman P. Amarasinghe
Seq: a high-performance language for bioinformatics. Proc. ACM Program. Lang. 3 (OOPSLA) (2019)
Tristan Bepler, Bonnie Berger
Learning protein sequence embeddings using information from structure. ICLR (Poster) (2019)
Hyunghoon Cho, Bonnie Berger, Jian Peng
Generalizable Visualization of Mega-Scale Single-Cell Data. RECOMB (2018)
Hooman Zabeti, Tamon Stephen, Bonnie Berger, Leonid Chindelevitch
A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models. WABI (2018)
Yaron Orenstein, Yun William Yu, Bonnie Berger
-Mers Using Joker Characters. J. Comput. Biol. 25 (11) (2018)
Ariya Shajii, Ibrahim Numanagic, Bonnie Berger
Latent Variable Model for Aligning Barcoded Short-Reads Improves Downstream Analyses. RECOMB (2018)
Tristan Bepler, Andrew Morin, Alex J. Noble, Julia Brasch, Lawrence Shapiro, Bonnie Berger
Positive-Unlabeled Convolutional Neural Networks for Particle Picking in Cryo-electron Micrographs. RECOMB (2018)
Ibrahim Numanagic, Alim S. Gökkaya, Lillian Zhang, Bonnie Berger, Can Alkan, Faraz Hach
Fast Characterization of Segmental Duplications in Genome Assemblies. CoRR (2018)
Tristan Bepler, Andrew Morin, Alex J. Noble, Julia Brasch, Lawrence Shapiro, Bonnie Berger
Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. CoRR (2018)
Ibrahim Numanagic, Alim S. Gökkaya, Lillian Zhang, Bonnie Berger, Can Alkan, Faraz Hach
Fast characterization of segmental duplications in genome assemblies. Bioinform. 34 (17) (2018)
Hyunghoon Cho, Benjamin Demeo, Jian Peng, Bonnie Berger
Large-Margin Classification in Hyperbolic Space. CoRR (2018)
Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
2017 ISCB Accomplishment by a Senior Scientist Award given to Pavel Pevzner. PLoS Comput. Biol. 13 (6) (2017)
Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
2017 ISCB Innovator Award: Aviv Regev. F1000Research 6 (2017)
Cheng-Yu Ma, Yi-Ping Phoebe Chen, Bonnie Berger, Chung-Shou Liao
Identification of protein complexes by integrating multiple alignment of protein interaction networks. Bioinform. 33 (11) (2017)
Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
2017 Outstanding Contributions to ISCB Award: Fran Lewitter. PLoS Comput. Biol. 13 (6) (2017)
Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
2017 Outstanding Contributions to ISCB Award: Fran Lewitter. F1000Research 6 (2017)
Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
2017 ISCB Overton Prize: Christoph Bock. F1000Research 6 (2017)
Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
2017 ISCB Overton Prize awarded to Christoph Bock. PLoS Comput. Biol. 13 (6) (2017)
Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
2017 ISCB Innovator Award: Aviv Regev. PLoS Comput. Biol. 13 (6) (2017)
Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
Message from the ISCB: 2017 Outstanding Contributions to ISCB Award Given to Fran Lewitter. Bioinform. 33 (14) (2017)
Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
Message from the ISCB: 2017 ISCB Accomplishment by a Senior Scientist Award Given to Pavel Pevzner. Bioinform. 33 (14) (2017)
Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
Message from the ISCB: 2017 ISCB Innovator Award Given to Aviv Regev. Bioinform. 33 (14) (2017)
Bonnie Berger, Terry Gaasterland, Thomas Lengauer, Christine A. Orengo, Bruno Gaëta, Scott Markel, Alfonso Valencia
ISCB's initial reaction to New England Journal of Medicine editorial on data sharing. Bioinform. 33 (18) (2017)
Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
2017 ISCB Accomplishment by a Senior Scientist Award: Pavel Pevzner. F1000Research 6 (2017)
Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
Message from the ISCB: 2017 ISCB Overton Prize Awarded to Christoph Bock. Bioinform. 33 (14) (2017)
Yaron Orenstein, Ryan Kim, Polly Fordyce, Bonnie Berger
Joker de Bruijn: Sequence Libraries to Cover All k-mers Using Joker Characters. RECOMB (2017)
Sean Simmons, Bonnie Berger
Realizing privacy preserving genome-wide association studies. Bioinform. 32 (9) (2016)
Claudio Alberti, Noah M. Daniels, Mikel Hernaez, Jan Voges, Rachel L. Goldfeder, Ana A. Hernandez-Lopez, Marco Mattavelli, Bonnie Berger
An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values. DCC (2016)
Yaron Orenstein, Bonnie Berger
-mers. J. Comput. Biol. 23 (2) (2016)
Bonnie Berger, Noah M. Daniels
Computational biology in the 21st century: scaling with compressive algorithms. Commun. ACM 59 (8) (2016)
Yunan Luo, Jianyang Zeng, Bonnie Berger, Jian Peng
Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning. RECOMB (2016)
Sean Simmons, Cenk S. Sahinalp, Bonnie Berger
Enabling Privacy Preserving GWAS in Heterogeneous Human Populations. RECOMB (2016)
Bonnie Berger, Terry Gaasterland, Thomas Lengauer, Christine A. Orengo, Bruno Gaëta, Scott Markel, Alfonso Valencia
Editorial on Data Sharing. PLoS Comput. Biol. 12 (3) (2016)
Yaron Orenstein, Yuhao Wang, Bonnie Berger
RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data. Bioinform. 32 (12) (2016)
Ariya Shajii, Deniz Yörükoglu, Yun William Yu, Bonnie Berger
-mer matching. Bioinform. 32 (17) (2016)
Yaron Orenstein, Bonnie Berger
Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers. WABI (2015)
Peter D. Karp, Bonnie Berger, Diane E. Kovats, Thomas Lengauer, Michal Linial, Pardis Sabeti, Winston Hide, Burkhard Rost
Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus. Bioinform. 31 (4) (2015)
Hyunghoon Cho, Bonnie Berger, Jian Peng
Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks. RECOMB (2015)
Peter D. Karp, Bonnie Berger, Diane E. Kovats, Thomas Lengauer, Michal Linial, Pardis Sabeti, Winston Hide, Burkhard Rost
ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus. PLoS Comput. Biol. 11 (1) (2015)
Hyunghoon Cho, Bonnie Berger, Jian Peng
Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks. CoRR (2015)
Emily Berger, Deniz Yörükoglu, Bonnie Berger
HapTree-X: An Integrative Bayesian Framework for Haplotype Reconstruction from Transcriptome and Genome Sequencing Data. RECOMB (2015)
Sheng Wang, Hyunghoon Cho, ChengXiang Zhai, Bonnie Berger, Jian Peng
Exploiting ontology graph for predicting sparsely annotated gene function. Bioinform. 31 (12) (2015)
Yun William Yu, Noah M. Daniels, David Christian Danko, Bonnie Berger
Entropy-scaling search of massive biological data. CoRR (2015)
Sean Simmons, Bonnie Berger
One Size Doesn't Fit All: Measuring Individual Privacy in Aggregate Genomic Data. IEEE Symposium on Security and Privacy Workshops (2015)
Sean Simmons, Jian Peng, Jadwiga R. Bienkowska, Bonnie Berger
Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data. J. Comput. Biol. 22 (8) (2015)
Yun William Yu, Deniz Yörükoglu, Bonnie Berger
Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification. RECOMB (2014)
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, Herbert M. Sauro, Gustavo Stolovitzky, Julio Saez-Rodriguez
Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. BMC Syst. Biol. 8 (2014)
Emily Berger, Deniz Yörükoglu, Jian Peng, Bonnie Berger
HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data. PLoS Comput. Biol. 10 (3) (2014)
Emily Berger, Deniz Yörükoglu, Jian Peng, Bonnie Berger
HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data. RECOMB (2014)
Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger
Simultaneous Alignment and Folding of Protein Sequences. J. Comput. Biol. 21 (7) (2014)
Noah M. Daniels, Andrew Gallant, Jian Peng, Lenore J. Cowen, Michael Baym, Bonnie Berger
Compressive genomics for protein databases. Bioinform. 29 (13) (2013)
George Tucker, Po-Ru Loh, Bonnie Berger
A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis. BMC Bioinform. 14 (2013)
Leonid Chindelevitch, Cheng-Yu Ma, Chung-Shou Liao, Bonnie Berger
Optimizing a global alignment of protein interaction networks. Bioinform. 29 (21) (2013)
Cheng-Yu Ma, Shu-Hsi Lin, Chi-Ching Lee, Chuan Yi Tang, Bonnie Berger, Chung-Shou Liao
Reconstruction of phyletic trees by global alignment of multiple metabolic networks. BMC Bioinform. 14 (S-2) (2013)
Patrick R. Schmid, Nathan P. Palmer, Isaac S. Kohane, Bonnie Berger
Making sense out of massive data by going beyond differential expression. Proc. Natl. Acad. Sci. USA 109 (15) (2012)
Noah M. Daniels, Raghavendra Hosur, Bonnie Berger, Lenore J. Cowen
SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone. Bioinform. 28 (9) (2012)
Leonid Chindelevitch, Po-Ru Loh, Ahmed Enayetallah, Bonnie Berger, Daniel Ziemek
Assessing statistical significance in causal graphs. BMC Bioinform. 13 (2012)
Bonnie Berger
Editorial. Bioinform. 28 (12) (2012)
Sebastian Will, Michael Yu, Bonnie Berger
Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAs. RECOMB (2012)
Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger, Jérôme Waldispühl
Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models. J. Comput. Biol. 18 (11) (2011)
Charles W. O'Donnell, Jérôme Waldispühl, Mieszko Lis, Randal Halfmann, Srinivas Devadas, Susan Lindquist, Bonnie Berger
A method for probing the mutational landscape of amyloid structure. Bioinform. 27 (13) (2011)
Yanhui Hu, Ian Flockhart, Arunachalam Vinayagam, Clemens Bergwitz, Bonnie Berger, Norbert Perrimon, Stephanie E. Mohr
An Integrative Approach to Ortholog Prediction for Disease-Focused and Other Functional Studies. BMC Bioinform. 12 (2011)
Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger, Jérôme Waldispühl
Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models. RECOMB (2011)
Leonid Chindelevitch, Aviv Regev, Bonnie Berger
Metabolic Network Analysis Demystified. RECOMB (2011)

Bonnie Berger.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Bonnie Berger