Approximation Algorithms for the Maximum Acyclic Subgraph Problem. - Bonnie Berger; Peter W. Shor (SODA, 1990)

A Better Performance Guarantee for Approximate Graph Coloring. - Bonnie Berger; John Rompel (Algorithmica, 1990)

Complexity Results and Algorithms for { <, <=, = }-Constrained Scheduling. - Bonnie Berger; Lenore Cowen (SODA, 1991)

Simulating (log c n)-Wise Independence in NC. - Bonnie Berger; John Rompel (J. ACM, 1991)

Fast Network Decomposition (Extended Abstract). - Baruch Awerbuch; Bonnie Berger; Lenore Cowen; David Peleg (PODC, 1992)

Near-Linear Cost Sequential and Distribured Constructions of Sparse Neighborhood Covers - Baruch Awerbuch; Bonnie Berger; Lenore Cowen; David Peleg (FOCS, 1993)

Efficient NC Algorithms for Set Cover with Applications to Learning and Geometry. - Bonnie Berger; John Rompel; Peter W. Shor (J. Comput. Syst. Sci., 1994)

Low-Diameter Graph Decomposition Is in NC. - Baruch Awerbuch; Bonnie Berger; Lenore Cowen; David Peleg (Random Struct. Algorithms, 1994)

Improved Algorithms for Protein Motif Recognition. - Bonnie Berger; David Bruce Wilson (SODA, 1995)

Nearly Optimal Algorithms and Bounds for Multilayer Channel Routing. - Bonnie Berger; Martin L. Brady; Donna J. Brown; Frank Thomson Leighton (J. ACM, 1995)

Scheduling with Concurrency-Based Constraints. - Bonnie Berger; Lenore Cowen (J. Algorithms, 1995)

Algorithms for Protein Structural Motif Recognition. - Bonnie Berger (J. Comput. Biol., 1995)

Fast Distributed Network Decompositions and Covers. - Baruch Awerbuch; Bonnie Berger; Lenore Cowen; David Peleg (J. Parallel Distributed Comput., 1996)

Tight Bounds for the Maximum Acyclic Subgraph Problem. - Bonnie Berger; Peter W. Shor (J. Algorithms, 1997)

An Iterative Method for Improved Protein Structural Motif Recognition. - Bonnie Berger; Mona Singh 001 (J. Comput. Biol., 1997)

The Fourth Moment Method. - Bonnie Berger (SIAM J. Comput., 1997)

Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete. - Bonnie Berger; Frank Thomson Leighton (RECOMB, 1998)

Protein Folding in the Hydrophobic-Hydrophilic(HP) Model is NP-Complete. - Bonnie Berger; Frank Thomson Leighton (J. Comput. Biol., 1998)

Computational learning reveals coiled coil-like motifs in histidine kinase linker domains. - Mona Singh 001; Bonnie Berger; Peter S. Kim; James M. Berger; Andrea G. Cochran (Proc. Natl. Acad. Sci. USA, 1998)

Near-Linear Time Construction of Sparse Neighborhood Covers. - Baruch Awerbuch; Bonnie Berger; Lenore Cowen; David Peleg (SIAM J. Comput., 1998)

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 (RECOMB, 1999)

Reconstructing a Three-Dimensional Model with Arbitrary Errors. - Bonnie Berger; Jon M. Kleinberg; Frank Thomson Leighton (J. ACM, 1999)

On the Structure of the Scaffolding Core of Bacteriophage T4. - Bonnie Berger; G. W. Hoest; J. R. Paulson; Peter W. Shor (J. Comput. Biol., 1999)

A Dictionary-Based Approach for Gene Annotation. - Lior Pachter; Serafim Batzoglou; Valentin I. Spitkovsky; Eric Banks; Eric S. Lander; Daniel J. Kleitman; Bonnie Berger (J. Comput. Biol., 1999)

Sequencing a genome by walking with clone-end sequences: a mathematical analysis (abstract). - Serafim Batzoglou; Bonnie Berger; Jill P. Mesirov; Eric S. Lander (RECOMB, 2000)

Human and mouse gene structure: comparative analysis and application to exon prediction. - Serafim Batzoglou; Lior Pachter; Jill P. Mesirov; Bonnie Berger; Eric S. Lander (RECOMB, 2000)

Local rule mechanism for selecting icosahedral shell geometry. - Bonnie Berger; Jonathan A. King; Russell Schwartz; Peter W. Shor (Discret. Appl. Math., 2000)

Trilogy: discovery of sequence-structure patterns across diverse proteins. - Phil Bradley; Peter S. Kim; Bonnie Berger (RECOMB, 2002)

Predicting the Beta-Helix Fold from Protein Sequence Data. - Lenore Cowen; Phil Bradley; Matthew Menke; Jonathan King; Bonnie Berger (J. Comput. Biol., 2002)

Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species. - Manolis Kamvysselis; Nick Patterson; Bruce Birren; Bonnie Berger; Eric S. Lander (RECOMB, 2003)

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 (RECOMB, 2004)

Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery. - Manolis Kellis; Nick Patterson; Bruce Birren; Bonnie Berger; Eric S. Lander (J. Comput. Biol., 2004)

msari. - Alex Coventry; Daniel J. Kleitman; Bonnie Berger (Proc. Natl. Acad. Sci. USA, 2004)

A Tree-Decomposition Approach to Protein Structure Prediction. - Jinbo Xu; Feng Jiao; Bonnie Berger (CSB, 2005)

Active learning for sampling in time-series experiments with application to gene expression analysis. - Rohit Singh 001; Nathan P. Palmer; David K. Gifford; Bonnie Berger; Ziv Bar-Joseph (ICML, 2005)

ChainTweak: Sampling from the Neighbourhood of a Protein Conformation. - Rohit Singh 001; Bonnie Berger (Pacific Symposium on Biocomputing, 2005)

Wrap-and-Pack: A New Paradigm for Beta Structural Motif Recognition with Application to Recognizing Beta Trefoils. - Matthew Menke; Jonathan King; Bonnie Berger; Lenore Cowen (J. Comput. Biol., 2005)

Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction. - Rohit Singh 001; Jinbo Xu; Bonnie Berger (Pacific Symposium on Biocomputing, 2006)

Paircoil2: improved prediction of coiled coils from sequence. - A. V. McDonnell; Taijiao Jiang; Amy E. Keating; Bonnie Berger (Bioinform., 2006)

Fast and accurate algorithms for protein side-chain packing. - Jinbo Xu; Bonnie Berger (J. ACM, 2006)

transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels. - Jérôme Waldispühl; Bonnie Berger; Peter Clote; Jean-Marc Steyaert (Nucleic Acids Res., 2006)

Lthreader: Prediction of Ligand-Receptor Interactions Using Localized Threading. - Vinay Pulim; Jadwiga R. Bienkowska; Bonnie Berger (Pacific Symposium on Biocomputing, 2007)

Probabilistic Modeling of Systematic Errors in Two-Hybrid Experiments. - David A. Sontag; Rohit Singh 001; Bonnie Berger (Pacific Symposium on Biocomputing, 2007)

Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology. - Rohit Singh 001; Jinbo Xu; Bonnie Berger (RECOMB, 2007)

Predicting and Annotating Catalytic Residues: An Information Theoretic Approach. - Beckett W. Sterner; Rohit Singh 001; Bonnie Berger (J. Comput. Biol., 2007)

A Parameterized Algorithm for Protein Structure Alignment. - Jinbo Xu; Feng Jiao; Bonnie Berger (J. Comput. Biol., 2007)

Automated real time constant-specificity surveillance for disease outbreaks. - Shannon C. Wieland; John S. Brownstein; Bonnie Berger; Kenneth D. Mandl (BMC Medical Informatics Decis. Mak., 2007)

Inverting the Viterbi algorithm: an abstract framework for structure design. - Michael Schnall-Levin; Leonid Chindelevitch; Bonnie Berger (ICML, 2008)

Global Alignment of Multiple Protein Interaction Networks. - Rohit Singh 001; Jinbo Xu; Bonnie Berger (Pacific Symposium on Biocomputing, 2008)

High-Resolution Modeling of Cellular Signaling Networks. - Michael Baym; Chris Bakal; Norbert Perrimon; Bonnie Berger (RECOMB, 2008)

Graph algorithms for biological systems analysis. - Bonnie Berger; Rohit Singh 001; Jinbo Xu (SODA, 2008)

Optimal contact map alignment of protein-protein interfaces. - Vinay Pulim; Bonnie Berger; Jadwiga R. Bienkowska (Bioinform., 2008)

Matt: Local Flexibility Aids Protein Multiple Structure Alignment. - Matthew Menke; Bonnie Berger; Lenore Cowen (PLoS Comput. Biol., 2008)

Efficient Algorithms for Probing the RNA Mutation Landscape. - Jérôme Waldispühl; Srinivas Devadas; Bonnie Berger; Peter Clote (PLoS Comput. Biol., 2008)

Global alignment of multiple protein interaction networks with application to functional orthology detection. - Rohit Singh 001; Jinbo Xu; Bonnie Berger (Proc. Natl. Acad. Sci. USA, 2008)

IsoRankN: spectral methods for global alignment of multiple protein networks. - Chung-Shou Liao; Kanghao Lu; Michael Baym; Rohit Singh 001; Bonnie Berger (Bioinform., 2009)

RNAmutants: a web server to explore the mutational landscape of RNA secondary structures. - Jérôme Waldispühl; Srinivas Devadas; Bonnie Berger; Peter Clote (Nucleic Acids Res., 2009)

BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis. - Allen W. Bryan Jr.; Matthew Menke; Lenore J. Cowen; Susan Lindquist; Bonnie Berger (PLoS Comput. Biol., 2009)

Local Optimization for Global Alignment of Protein Interaction Networks. - Leonid Chindelevitch; Chung-Shou Liao; Bonnie Berger (Pacific Symposium on Biocomputing, 2010)

Struct2Net: a web service to predict protein-protein interactions using a structure-based approach. - Rohit Singh 001; Daniel Park; Jinbo Xu; Raghavendra Hosur; Bonnie Berger (Nucleic Acids Res., 2010)

Markov random fields reveal an N-terminal double beta-propeller motif as part of a bacterial hybrid two-component sensor system. - Matthew Menke; Bonnie Berger; Lenore Cowen (Proc. Natl. Acad. Sci. USA, 2010)

Metabolic Network Analysis Demystified. - Leonid Chindelevitch; Aviv Regev; Bonnie Berger (RECOMB, 2011)

Sparse estimation for structural variability. - Raghavendra Hosur; Rohit Singh 001; Bonnie Berger (Algorithms Mol. Biol., 2011)

A method for probing the mutational landscape of amyloid structure. - Charles W. O'Donnell; Jérôme Waldispühl; Mieszko Lis; Randal Halfmann; Srinivas Devadas; Susan Lindquist; Bonnie Berger (Bioinform., 2011)

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; Stephanie E. Mohr (BMC Bioinform., 2011)

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

Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models. - Solomon Shenker; Charles W. O'Donnell; Srinivas Devadas; Bonnie Berger; Jérôme Waldispühl (J. Comput. Biol., 2011)

IsoBase: a database of functionally related proteins across PPI networks. - Daniel Park; Rohit Singh 001; Michael Baym; Chung-Shou Liao; Bonnie Berger (Nucleic Acids Res., 2011)

Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAs. - Sebastian Will; Michael Yu; Bonnie Berger (RECOMB, 2012)

Editorial. - Bonnie Berger (Bioinform., 2012)

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; Lenore J. Cowen (Bioinform., 2012)

Assessing statistical significance in causal graphs. - Leonid Chindelevitch; Po-Ru Loh; Ahmed Enayetallah; Bonnie Berger; Daniel Ziemek (BMC Bioinform., 2012)

Making sense out of massive data by going beyond differential expression. - Patrick R. Schmid; Nathan P. Palmer; Isaac S. Kohane; Bonnie Berger (Proc. Natl. Acad. Sci. USA, 2012)

Optimizing a global alignment of protein interaction networks. - Leonid Chindelevitch; Cheng-Yu Ma; Chung-Shou Liao; Bonnie Berger (Bioinform., 2013)

Compressive genomics for protein databases. - Noah M. Daniels; Andrew Gallant; Jian Peng 001; Lenore J. Cowen; Michael Baym; Bonnie Berger (Bioinform., 2013)

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; Chung-Shou Liao (BMC Bioinform., 2013)

A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis. - George Tucker; Po-Ru Loh; Bonnie Berger (BMC Bioinform., 2013)

Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification. - Yun William Yu; Deniz Yörükoglu; Bonnie Berger (RECOMB, 2014)

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. - Pablo Meyer 001; Thomas Cokelaer; Deepak Chandran; Kyung Hyuk Kim; Po-Ru Loh; George Tucker; Mark Lipson; Bonnie Berger; Clemens Kreutz; Andreas Raue; Bernhard Steiert; Jens Timmer; et al. (BMC Syst. Biol., 2014)

Simultaneous Alignment and Folding of Protein Sequences. - Jérôme Waldispühl; Charles W. O'Donnell; Sebastian Will; Srinivas Devadas; Rolf Backofen; Bonnie Berger (J. Comput. Biol., 2014)

HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data. - Emily Berger; Deniz Yörükoglu; Jian Peng 001; Bonnie Berger (PLoS Comput. Biol., 2014)

HapTree-X: An Integrative Bayesian Framework for Haplotype Reconstruction from Transcriptome and Genome Sequencing Data. - Emily Berger; Deniz Yörükoglu; Bonnie Berger (RECOMB, 2015)

Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks. - Hyunghoon Cho; Bonnie Berger; Jian Peng 001 (RECOMB, 2015)

One Size Doesn't Fit All: Measuring Individual Privacy in Aggregate Genomic Data. - Sean Simmons 001; Bonnie Berger (IEEE Symposium on Security and Privacy Workshops, 2015)

Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers. - Yaron Orenstein; Bonnie Berger (WABI, 2015)

Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus. - Peter D. Karp; Bonnie Berger; Diane E. Kovats; Thomas Lengauer; Michal Linial; Pardis Sabeti; Winston Hide; Burkhard Rost (Bioinform., 2015)

Exploiting ontology graph for predicting sparsely annotated gene function. - Sheng Wang 001; Hyunghoon Cho; ChengXiang Zhai; Bonnie Berger; Jian Peng 001 (Bioinform., 2015)

Entropy-scaling search of massive biological data. - Yun William Yu; Noah M. Daniels; David Christian Danko; Bonnie Berger (CoRR, 2015)

Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data. - Sean Simmons 001; Jian Peng 001; Jadwiga R. Bienkowska; Bonnie Berger (J. Comput. Biol., 2015)

ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus. - Peter D. Karp; Bonnie Berger; Diane E. Kovats; Thomas Lengauer; Michal Linial; Pardis Sabeti; Winston Hide; Burkhard Rost (PLoS Comput. Biol., 2015)

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 (DCC, 2016)

Enabling Privacy Preserving GWAS in Heterogeneous Human Populations. - Sean Simmons 001; S. Cenk Sahinalp; Bonnie Berger (RECOMB, 2016)

Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning. - Yunan Luo; Jianyang Zeng 001; Bonnie Berger; Jian Peng 001 (RECOMB, 2016)

RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data. - Yaron Orenstein; Yuhao Wang; Bonnie Berger (Bioinform., 2016)

Fast genotyping of known SNPs through approximate k-mer matching. - Ariya Shajii; Deniz Yörükoglu; Yun William Yu; Bonnie Berger (Bioinform., 2016)

Realizing privacy preserving genome-wide association studies. - Sean Simmons 001; Bonnie Berger (Bioinform., 2016)

Computational biology in the 21st century: scaling with compressive algorithms. - Bonnie Berger; Noah M. Daniels (Commun. ACM, 2016)

Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers. - Yaron Orenstein; Bonnie Berger (J. Comput. Biol., 2016)

ISCB's Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing. - Bonnie Berger; Terry Gaasterland; Thomas Lengauer; Christine A. Orengo; Bruno Gaëta; Scott Markel; Alfonso Valencia (PLoS Comput. Biol., 2016)

Joker de Bruijn: Sequence Libraries to Cover All k-mers Using Joker Characters. - Yaron Orenstein; Ryan Kim; Polly Fordyce; Bonnie Berger (RECOMB, 2017)

ISCB's initial reaction to New England Journal of Medicine editorial on data sharing. - Bonnie Berger; Terry Gaasterland; Thomas Lengauer; Christine A. Orengo; Bruno Gaëta; Scott Markel; Alfonso Valencia (Bioinform., 2017)

Message from the ISCB: 2017 ISCB Innovator Award Given to Aviv Regev. - Christiana N. Fogg; Diane E. Kovats; Bonnie Berger (Bioinform., 2017)

Message from the ISCB: 2017 ISCB Accomplishment by a Senior Scientist Award Given to Pavel Pevzner. - Christiana N. Fogg; Diane E. Kovats; Bonnie Berger (Bioinform., 2017)

Message from the ISCB: 2017 ISCB Overton Prize Awarded to Christoph Bock. - Christiana N. Fogg; Diane E. Kovats; Bonnie Berger (Bioinform., 2017)

Message from the ISCB: 2017 Outstanding Contributions to ISCB Award Given to Fran Lewitter. - Christiana N. Fogg; Diane E. Kovats; Bonnie Berger (Bioinform., 2017)

Identification of protein complexes by integrating multiple alignment of protein interaction networks. - Cheng-Yu Ma; Yi-Ping Phoebe Chen; Bonnie Berger; Chung-Shou Liao (Bioinform., 2017)

2017 ISCB Accomplishment by a Senior Scientist Award: Pavel Pevzner. - Christiana N. Fogg; Diane E. Kovats; Bonnie Berger (F1000Research, 2017)

2017 ISCB Overton Prize: Christoph Bock. - Christiana N. Fogg; Diane E. Kovats; Bonnie Berger (F1000Research, 2017)

2017 ISCB Accomplishment by a Senior Scientist Award given to Pavel Pevzner. - Christiana N. Fogg; Diane E. Kovats; Bonnie Berger (PLoS Comput. Biol., 2017)

2017 Outstanding Contributions to ISCB Award: Fran Lewitter. - Christiana N. Fogg; Diane E. Kovats; Bonnie Berger (PLoS Comput. Biol., 2017)

2017 ISCB Overton Prize awarded to Christoph Bock. - Christiana N. Fogg; Diane E. Kovats; Bonnie Berger (PLoS Comput. Biol., 2017)

2017 ISCB Innovator Award: Aviv Regev. - Christiana N. Fogg; Diane E. Kovats; Bonnie Berger (PLoS Comput. Biol., 2017)

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 (RECOMB, 2018)

Generalizable Visualization of Mega-Scale Single-Cell Data. - Hyunghoon Cho; Bonnie Berger; Jian Peng 001 (RECOMB, 2018)

Latent Variable Model for Aligning Barcoded Short-Reads Improves Downstream Analyses. - Ariya Shajii; Ibrahim Numanagic; Bonnie Berger (RECOMB, 2018)

A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models. - Hooman Zabeti; Tamon Stephen; Bonnie Berger; Leonid Chindelevitch (WABI, 2018)

Fast characterization of segmental duplications in genome assemblies. - Ibrahim Numanagic; Alim S. Gökkaya; Lillian Zhang; Bonnie Berger; Can Alkan; Faraz Hach (Bioinform., 2018)

Joker de Bruijn: Covering k-Mers Using Joker Characters. - Yaron Orenstein; Yun William Yu; Bonnie Berger (J. Comput. Biol., 2018)

Large-Margin Classification in Hyperbolic Space. - Hyunghoon Cho; Benjamin Demeo; Jian Peng 001; Bonnie Berger (AISTATS, 2019)

Learning protein sequence embeddings using information from structure. - Tristan Bepler; Bonnie Berger (ICLR (Poster), 2019)

Explicitly disentangling image content from translation and rotation with spatial-VAE. - Tristan Bepler; Ellen D. Zhong; Kotaro Kelley; Edward Brignole; Bonnie Berger (NeurIPS, 2019)

Protecting Genomic Data Privacy with Probabilistic Modeling. - Sean Simmons 001; Bonnie Berger; S. Cenk Sahinalp (PSB, 2019)

Geometric Sketching of Single-Cell Data Preserves Transcriptional Structure. - Brian Hie; Hyunghoon Cho; Benjamin Demeo; Bryan Bryson; Bonnie Berger (RECOMB, 2019)

Metagenomic binning through low-density hashing. - Yunan Luo; Yun William Yu; Jianyang Zeng 001; Bonnie Berger; Jian Peng 001 (Bioinform., 2019)

Reconstructing continuously heterogeneous structures from single particle cryo-EM with deep generative models. - Ellen D. Zhong; Tristan Bepler; Joseph H. Davis; Bonnie Berger (CoRR, 2019)

Seq: a high-performance language for bioinformatics. - Ariya Shajii; Ibrahim Numanagic; Riyadh Baghdadi; Bonnie Berger; Saman P. Amarasinghe (Proc. ACM Program. Lang., 2019)

Seq (OOPSLA 2019 Artifact). - Ariya Shajii; Ibrahim Numanagic; Riyadh Baghdadi; Bonnie Berger; Saman P. Amarasinghe (Zenodo, 2019)

Reconstructing continuous distributions of 3D protein structure from cryo-EM images. - Ellen D. Zhong; Tristan Bepler; Joseph H. Davis; Bonnie Berger (ICLR, 2020)

Learning Mutational Semantics. - Brian Hie; Ellen D. Zhong; Bryan Bryson; Bonnie Berger (NeurIPS, 2020)

Privacy-Preserving Biomedical Database Queries with Optimal Privacy-Utility Trade-Offs. - Hyunghoon Cho; Sean Simmons 001; Ryan Kim; Bonnie Berger (RECOMB, 2020)

A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets. - Baris Ekim; Bonnie Berger; Yaron Orenstein (RECOMB, 2020)

Hopper: a mathematically optimal algorithm for sketching biological data. - Benjamin Demeo; Bonnie Berger (Bioinform., 2020)

scVAE: variational auto-encoders for single-cell gene expression data. - Christopher Heje Grønbech; Maximillian Fornitz Vording; Pascal N. Timshel; Casper Kaae Sønderby; Tune H. Pers; Ole Winther; Bonnie Berger (Bioinform., 2020)

Meta-analysis of Caenorhabditis elegans single-cell developmental data reveals multi-frequency oscillation in gene activation. - Luke A. D. Hutchison; Bonnie Berger; Isaac S. Kohane (Bioinform., 2020)

CryoDRGN2: Ab initio neural reconstruction of 3D protein structures from real cryo-EM images. - Ellen D. Zhong; Adam Lerer; Joseph H. Davis; Bonnie Berger (ICCV, 2021)

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 (ICLR, 2021)

Bayesian information sharing enhances detection of regulatory associations in rare cell types. - Alexander P. Wu; Jian Peng 001; Bonnie Berger; Hyunghoon Cho (Bioinform., 2021)

Levenshtein Distance, Sequence Comparison and Biological Database Search. - Bonnie Berger; Michael S. Waterman; Yun William Yu (IEEE Trans. Inf. Theory, 2021)

Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalities. - Rohit Singh 001; Brian Hie; Ashwin Narayan; Bonnie Berger (Zenodo, 2021)

virDTL. - Sumaira Zaman; Samuel Sledzieski; Bonnie Berger; Yi-Chieh Wu; Mukul S. Bansal (Zenodo, 2021)

Granger causal inference on DAGs identifies genomic loci regulating transcription. - Alexander P. Wu; Rohit Singh 001; Bonnie Berger (ICLR, 2022)

Sequre: a high-performance framework for rapid development of secure bioinformatics pipelines. - Haris Smajlovic; Ariya Shajii; Bonnie Berger; Hyunghoon Cho; Ibrahim Numanagic (IPDPS Workshops, 2022)

Topsy-Turvy: integrating a global view into sequence-based PPI prediction. - Rohit Singh 001; Kapil Devkota; Samuel Sledzieski; Bonnie Berger; Lenore Cowen (Bioinform., 2022)

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 (CC, 2023)

Scalable and Privacy-Preserving Federated Principal Component Analysis. - David Froelicher; Hyunghoon Cho; Manaswitha Edupalli; Joao Sa Sousa; Jean-Philippe Bossuat; Apostolos Pyrgelis; Juan Ramón Troncoso-Pastoriza; Bonnie Berger; Jean-Pierre Hubaux (SP, 2023)

EigenFold: Generative Protein Structure Prediction with Diffusion Models. - Bowen Jing; Ezra Erives; Peter Pao-Huang; Gabriele Corso; Bonnie Berger; Tommi S. Jaakkola (CoRR, 2023)

virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2. - Sumaira Zaman; Samuel Sledzieski; Bonnie Berger; Yi-Chieh Wu; Mukul S. Bansal (J. Comput. Biol., 2023)

Causally-guided Regularization of Graph Attention Improves Generalizability. - Alexander P. Wu; Thomas Markovich; Bonnie Berger; Nils Yannick Hammerla; Rohit Singh 001 (Trans. Mach. Learn. Res., 2023)

sfkit: a web-based toolkit for secure and federated genomic analysis. - Simon Mendelsohn; David Froelicher; Denis Loginov; David Bernick; Bonnie Berger; Hyunghoon Cho (Nucleic Acids Res., 2023)

TT3D: Leveraging precomputed protein 3D sequence models to predict protein-protein interactions. - Samuel Sledzieski; Kapil Devkota; Rohit Singh 001; Lenore Cowen; Bonnie Berger (Bioinform., 2023)

Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms. - Bowen Jing; Tommi S. Jaakkola; Bonnie Berger (ICLR, 2024)

AlphaFold Meets Flow Matching for Generating Protein Ensembles. - Bowen Jing; Bonnie Berger; Tommi S. Jaakkola (ICML, 2024)

Dirichlet Flow Matching with Applications to DNA Sequence Design. - Hannes Stärk; Bowen Jing; Chenyu Wang 003; Gabriele Corso; Bonnie Berger; Regina Barzilay; Tommi S. Jaakkola (ICML, 2024)

Generative Modeling of Molecular Dynamics Trajectories. - Bowen Jing; Hannes Stärk; Tommi S. Jaakkola; Bonnie Berger (NeurIPS, 2024)

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 (RECOMB, 2024)

ralphi: A Deep Reinforcement Learning Framework for Haplotype Assembly. - Enzo Battistella; Anant Maheshwari; Baris Ekim; Bonnie Berger; Victoria Popic (RECOMB, 2025)

Decoding the Functional Interactome of Non-model Organisms with PHILHARMONIC. - Samuel Sledzieski; Charlotte Versavel; Rohit Singh 001; Faith Ocitti; Kapil Devkota; Lokender Kumar; Polina Shpilker; Liza Roger; Jinkyu Yang; Nastassja Lewinski; Hollie Putnam; Bonnie Berger; et al. (RECOMB, 2025)

Shechi: A Secure Distributed Computation Compiler Based on Multiparty Homomorphic Encryption. - Haris Smajlovic; David Froelicher; Ariya Shajii; Bonnie Berger; Hyunghoon Cho; Ibrahim Numanagic (Zenodo, 2025)

Shechi: A Secure Distributed Computation Compiler Based on Multiparty Homomorphic Encryption. - Haris Smajlovic; David Froelicher; Ariya Shajii; Bonnie Berger; Hyunghoon Cho; Ibrahim Numanagic (Zenodo, 2025)

Shechi: A Secure Distributed Computation Compiler Based on Multiparty Homomorphic Encryption. - Haris Smajlovic; David Froelicher; Ariya Shajii; Bonnie Berger; Hyunghoon Cho; Ibrahim Numanagic (Zenodo, 2025)

Shechi: A Secure Distributed Computation Compiler Based on Multiparty Homomorphic Encryption. - Haris Smajlovic; David Froelicher; Ariya Shajii; Bonnie Berger; Hyunghoon Cho; Ibrahim Numanagic (Zenodo, 2025)

Evaluating multiple models using labeled and unlabeled data. - Divya Shanmugam; Shuvom Sadhuka; Manish Raghavan; John V. Guttag; Bonnie Berger; Emma Pierson (CoRR, 2025)

Shechi: A Secure Distributed Computation Compiler Based on Multiparty Homomorphic Encryption. - Haris Smajlovic; David Froelicher; Ariya Shajii; Bonnie Berger; Hyunghoon Cho; Ibrahim Numanagic (Zenodo, 2025)

Urban Incident Prediction with Graph Neural Networks: Integrating Government Ratings and Crowdsourced Reports. - Sidhika Balachandar; Shuvom Sadhuka; Bonnie Berger; Emma Pierson; Nikhil Garg 001 (CoRR, 2025)