| 2026 | AAAI | Urban Incident Prediction with Graph Neural Networks: Integrating Government Ratings and Crowdsourced Reports. | Sidhika Balachandar, Shuvom Sadhuka, Bonnie Berger, Emma Pierson, Nikhil Garg |
| 2025 | FOCS | Efficiently Batching Unambiguous Interactive Proofs. | Bonnie Berger, Rohan Goyal, Matthew M. Hong, Yael Tauman Kalai |
| 2025 | RECOMB | ralphi: A Deep Reinforcement Learning Framework for Haplotype Assembly. | Enzo Battistella, Anant Maheshwari, Baris Ekim, Bonnie Berger, Victoria Popic |
| 2025 | RECOMB | Decoding the Functional Interactome of Non-model Organisms with PHILHARMONIC. | Samuel Sledzieski, Charlotte Versavel, Rohit Singh, Faith Ocitti, Kapil Devkota, Lokender Kumar, Polina Shpilker, Liza Roger, Jinkyu Yang, Nastassja Lewinski, Hollie Putnam, Bonnie Berger, Judith Klein-Seetharaman, Lenore Cowen |
| 2024 | ICLR | Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms. | Bowen Jing, Tommi S. Jaakkola, Bonnie Berger |
| 2024 | ICML | AlphaFold Meets Flow Matching for Generating Protein Ensembles. | Bowen Jing, Bonnie Berger, Tommi S. Jaakkola |
| 2024 | ICML | Dirichlet Flow Matching with Applications to DNA Sequence Design. | Hannes Strk, Bowen Jing, Chenyu Wang, Gabriele Corso, Bonnie Berger, Regina Barzilay, Tommi S. Jaakkola |
| 2024 | RECOMB | Secure Discovery of Genetic Relatives Across Large-Scale and Distributed Genomic Datasets. | Matthew M. Hong, David Froelicher, Ricky Magner, Victoria Popic, Bonnie Berger, Hyunghoon Cho |
| 2023 | CC | Codon: A Compiler for High-Performance Pythonic Applications and DSLs. | Ariya Shajii, Gabriel Ramirez, Haris Smajlovic, Jessica Ray, Bonnie Berger, Saman P. Amarasinghe, Ibrahim Numanagic |
| 2023 | SP | Scalable and Privacy-Preserving Federated Principal Component Analysis. | David Froelicher, Hyunghoon Cho, Manaswitha Edupalli, Joao Sa Sousa, Jean-Philippe Bossuat, Apostolos Pyrgelis, Juan Ramn Troncoso-Pastoriza, Bonnie Berger, Jean-Pierre Hubaux |
| 2022 | ICLR | Granger causal inference on DAGs identifies genomic loci regulating transcription. | Alexander P. Wu, Rohit Singh, Bonnie Berger |
| 2021 | ICCV | CryoDRGN2: Ab initio neural reconstruction of 3D protein structures from real cryo-EM images. | Ellen D. Zhong, Adam Lerer, Joseph H. Davis, Bonnie Berger |
| 2021 | ICLR | Multi-resolution modeling of a discrete stochastic process identifies causes of cancer. | Adam Uri Yaari, Maxwell Sherman, Oliver Clarke Priebe, Po-Ru Loh, Boris Katz, Andrei Barbu, Bonnie Berger |
| 2020 | ICLR | Reconstructing continuous distributions of 3D protein structure from cryo-EM images. | Ellen D. Zhong, Tristan Bepler, Joseph H. Davis, Bonnie Berger |
| 2020 | RECOMB | Privacy-Preserving Biomedical Database Queries with Optimal Privacy-Utility Trade-Offs. | Hyunghoon Cho, Sean Simmons, Ryan Kim, Bonnie Berger |
| 2020 | RECOMB | A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets. | Baris Ekim, Bonnie Berger, Yaron Orenstein |
| 2019 | AISTATS | Large-Margin Classification in Hyperbolic Space. | Hyunghoon Cho, Benjamin Demeo, Jian Peng, Bonnie Berger |
| 2019 | ICLR | Learning protein sequence embeddings using information from structure. | Tristan Bepler, Bonnie Berger |
| 2019 | PSB | Protecting Genomic Data Privacy with Probabilistic Modeling. | Sean Simmons, Bonnie Berger, S. Cenk Sahinalp |
| 2019 | RECOMB | Geometric Sketching of Single-Cell Data Preserves Transcriptional Structure. | Brian Hie, Hyunghoon Cho, Benjamin Demeo, Bryan Bryson, Bonnie Berger |
| 2018 | RECOMB | Positive-Unlabeled Convolutional Neural Networks for Particle Picking in Cryo-electron Micrographs. | Tristan Bepler, Andrew Morin, Alex J. Noble, Julia Brasch, Lawrence Shapiro, Bonnie Berger |
| 2018 | RECOMB | Generalizable Visualization of Mega-Scale Single-Cell Data. | Hyunghoon Cho, Bonnie Berger, Jian Peng |
| 2018 | RECOMB | Latent Variable Model for Aligning Barcoded Short-Reads Improves Downstream Analyses. | Ariya Shajii, Ibrahim Numanagic, Bonnie Berger |
| 2018 | WABI | A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models. | Hooman Zabeti, Tamon Stephen, Bonnie Berger, Leonid Chindelevitch |
| 2017 | RECOMB | Joker de Bruijn: Sequence Libraries to Cover All k-mers Using Joker Characters. | Yaron Orenstein, Ryan Kim, Polly Fordyce, Bonnie Berger |
| 2016 | DCC | An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values. | Claudio Alberti, Noah M. Daniels, Mikel Hernaez, Jan Voges, Rachel L. Goldfeder, Ana A. Hernandez-Lopez, Marco Mattavelli, Bonnie Berger |
| 2016 | RECOMB | Enabling Privacy Preserving GWAS in Heterogeneous Human Populations. | Sean Simmons, S. Cenk Sahinalp, Bonnie Berger |
| 2016 | RECOMB | Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning. | Yunan Luo, Jianyang Zeng, Bonnie Berger, Jian Peng |
| 2015 | RECOMB | HapTree-X: An Integrative Bayesian Framework for Haplotype Reconstruction from Transcriptome and Genome Sequencing Data. | Emily Berger, Deniz Yrkoglu, Bonnie Berger |
| 2015 | RECOMB | Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks. | Hyunghoon Cho, Bonnie Berger, Jian Peng |
| 2015 | SP | One Size Doesn't Fit All: Measuring Individual Privacy in Aggregate Genomic Data. | Sean Simmons, Bonnie Berger |
| 2015 | WABI | Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers. | Yaron Orenstein, Bonnie Berger |
| 2014 | RECOMB | HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data. | Emily Berger, Deniz Yrkoglu, Jian Peng, Bonnie Berger |
| 2014 | RECOMB | Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification. | Yun William Yu, Deniz Yrkoglu, Bonnie Berger |
| 2012 | RECOMB | Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAs. | Sebastian Will, Michael Yu, Bonnie Berger |
| 2011 | RECOMB | Metabolic Network Analysis Demystified. | Leonid Chindelevitch, Aviv Regev, Bonnie Berger |
| 2011 | RECOMB | Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models. | Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger, Jrme Waldisphl |
| 2010 | PSB | Local Optimization for Global Alignment of Protein Interaction Networks. | Leonid Chindelevitch, Chung-Shou Liao, Bonnie Berger |
| 2010 | WABI | Sparse Estimation for Structural Variability. | Raghavendra Hosur, Rohit Singh, Bonnie Berger |
| 2009 | RECOMB | Simultaneous Alignment and Folding of Protein Sequences. | Jrme Waldisphl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger |
| 2008 | ICML | Inverting the Viterbi algorithm: an abstract framework for structure design. | Michael Schnall-Levin, Leonid Chindelevitch, Bonnie Berger |
| 2008 | PSB | Global Alignment of Multiple Protein Interaction Networks. | Rohit Singh, Jinbo Xu, Bonnie Berger |
| 2008 | RECOMB | High-Resolution Modeling of Cellular Signaling Networks. | Michael Baym, Chris Bakal, Norbert Perrimon, Bonnie Berger |
| 2008 | SODA | Graph algorithms for biological systems analysis. | Bonnie Berger, Rohit Singh, Jinbo Xu |
| 2007 | PSB | Lthreader: Prediction of Ligand-Receptor Interactions Using Localized Threading. | Vinay Pulim, Jadwiga R. Bienkowska, Bonnie Berger |
| 2007 | PSB | Probabilistic Modeling of Systematic Errors in Two-Hybrid Experiments. | David A. Sontag, Rohit Singh, Bonnie Berger |
| 2007 | RECOMB | Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology. | Rohit Singh, Jinbo Xu, Bonnie Berger |
| 2006 | PSB | Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction. | Rohit Singh, Jinbo Xu, Bonnie Berger |
| 2006 | RECOMB | A Parameterized Algorithm for Protein Structure Alignment. | Jinbo Xu, Feng Jiao, Bonnie Berger |
| 2005 | ICML | Active learning for sampling in time-series experiments with application to gene expression analysis. | Rohit Singh, Nathan P. Palmer, David K. Gifford, Bonnie Berger, Ziv Bar-Joseph |
| 2005 | PSB | ChainTweak: Sampling from the Neighbourhood of a Protein Conformation. | Rohit Singh, Bonnie Berger |
| 2004 | RECOMB | Wrap-and-pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils. | Matthew Menke, Eben Scanlon, Jonathan King, Bonnie Berger, Lenore Cowen |
| 2003 | RECOMB | Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species. | Manolis Kamvysselis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric S. Lander |
| 2002 | RECOMB | Trilogy: discovery of sequence-structure patterns across diverse proteins. | Phil Bradley, Peter S. Kim, Bonnie Berger |
| 2001 | RECOMB | Predicting the beta-helix fold from protein sequence data. | Phil Bradley, Lenore Cowen, Matthew Menke, Jonathan King, Bonnie Berger |
| 2000 | RECOMB | Sequencing a genome by walking with clone-end sequences: a mathematical analysis (abstract). | Serafim Batzoglou, Bonnie Berger, Jill P. Mesirov, Eric S. Lander |
| 2000 | RECOMB | Human and mouse gene structure: comparative analysis and application to exon prediction. | Serafim Batzoglou, Lior Pachter, Jill P. Mesirov, Bonnie Berger, Eric S. Lander |
| 1999 | RECOMB | A dictionary based approach for gene annotation. | Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, William S. Beebee, Eric S. Lander, Bonnie Berger, Daniel J. Kleitman |
| 1998 | RECOMB | Protein folding in the hydrophobic-hydrophilic ( | Bonnie Berger, Frank Thomson Leighton |
| 1997 | RECOMB | An iterative method for improved protein structural motif recognition. | Bonnie Berger, Mona Singh |
| 1996 | STOC | Reconstructing a Three-Dimensional Model with Arbitrary Errors. | Bonnie Berger, Jon M. Kleinberg, Frank Thomson Leighton |
| 1995 | SODA | Improved Algorithms for Protein Motif Recognition. | Bonnie Berger, David Bruce Wilson |
| 1993 | FOCS | Near-Linear Cost Sequential and Distribured Constructions of Sparse Neighborhood Covers | Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg |
| 1992 | PODC | Fast Network Decomposition (Extended Abstract). | Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg |
| 1991 | SODA | The Fourth Moment Method. | Bonnie Berger |
| 1991 | SODA | Complexity Results and Algorithms for { <, <=, = }-Constrained Scheduling. | Bonnie Berger, Lenore Cowen |
| 1990 | SODA | Approximation Algorithms for the Maximum Acyclic Subgraph Problem. | Bonnie Berger, Peter W. Shor |
| 1989 | FOCS | Simulating (log ^c n)-wise Independence in NC | Bonnie Berger, John Rompel |
| 1989 | FOCS | Efficient NC Algorithms for Set Cover with Applications to Learning and Geometry | Bonnie Berger, John Rompel, Peter W. Shor |