Bonnie Berger - RankMe

193 papers A* 26A 1B 35C 3Misc 7Journal 116Unranked 5

Year	Rank	Type	Title / Venue / Authors
2026	A*	`conf`	Urban Incident Prediction with Graph Neural Networks: Integrating Government Ratings and Crowdsourced Reports. AAAI Sidhika Balachandar, Shuvom Sadhuka, Bonnie Berger, Emma Pierson, Nikhil Garg
2025	J	`jnl`	A Bayesian Model for Multi-stage Censoring. CoRR Shuvom Sadhuka, Sophia Lin, Bonnie Berger, Emma Pierson
2025	J	`jnl`	AI-based Methods for Simulating, Sampling, and Predicting Protein Ensembles. CoRR Bowen Jing, Bonnie Berger, Tommi S. Jaakkola
2025	B	`conf`	Decoding the Functional Interactome of Non-model Organisms with PHILHARMONIC. RECOMB 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
2025	A*	`conf`	Efficiently Batching Unambiguous Interactive Proofs. FOCS Bonnie Berger, Rohan Goyal, Matthew M. Hong, Yael Tauman Kalai
2025	J	`jnl`	Efficiently Batching Unambiguous Interactive Proofs. CoRR Bonnie Berger, Rohan Goyal, Matthew M. Hong, Yael Tauman Kalai
2025	J	`jnl`	Efficiently Batching Unambiguous Interactive Proofs. Electron. Colloquium Comput. Complex. Bonnie Berger, Rohan Goyal, Matthew M. Hong, Yael Tauman Kalai
2025	J	`jnl`	Evaluating multiple models using labeled and unlabeled data. CoRR Divya Shanmugam, Shuvom Sadhuka, Manish Raghavan, John V. Guttag, Bonnie Berger, Emma Pierson
2025	J	`jnl`	Learning residue level protein dynamics with multiscale Gaussians. CoRR Mihir Bafna, Bowen Jing, Bonnie Berger
2025	J	`jnl`	Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT. Bioinform. Daniel E. Schäffer, Samuel Sledzieski, Lenore Cowen, Bonnie Berger
2025	A*	`conf`	Shechi: A Secure Distributed Computation Compiler Based on Multiparty Homomorphic Encryption. USENIX Security Symposium Haris Smajlovic, David Froelicher, Ariya Shajii, Bonnie Berger, Hyunghoon Cho, Ibrahim Numanagic
2025	J	`jnl`	Urban Incident Prediction with Graph Neural Networks: Integrating Government Ratings and Crowdsourced Reports. CoRR Sidhika Balachandar, Shuvom Sadhuka, Bonnie Berger, Emma Pierson, Nikhil Garg
2025	B	`conf`	ralphi: A Deep Reinforcement Learning Framework for Haplotype Assembly. RECOMB Enzo Battistella, Anant Maheshwari, Baris Ekim, Bonnie Berger, Victoria Popic
2024	A*	`conf`	AlphaFold Meets Flow Matching for Generating Protein Ensembles. ICML Bowen Jing, Bonnie Berger, Tommi S. Jaakkola
2024	J	`jnl`	AlphaFold Meets Flow Matching for Generating Protein Ensembles. CoRR Bowen Jing, Bonnie Berger, Tommi S. Jaakkola
2024	A*	`conf`	Dirichlet Flow Matching with Applications to DNA Sequence Design. ICML Hannes Stärk, Bowen Jing, Chenyu Wang, Gabriele Corso, Bonnie Berger, Regina Barzilay, Tommi S. Jaakkola
2024	J	`jnl`	Dirichlet Flow Matching with Applications to DNA Sequence Design. CoRR Hannes Stärk, Bowen Jing, Chenyu Wang, Gabriele Corso, Bonnie Berger, Regina Barzilay, Tommi S. Jaakkola
2024	A*	`conf`	Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms. ICLR Bowen Jing, Tommi S. Jaakkola, Bonnie Berger
2024	A*	`conf`	Generative Modeling of Molecular Dynamics Trajectories. NeurIPS Bowen Jing, Hannes Stärk, Tommi S. Jaakkola, Bonnie Berger
2024	J	`jnl`	Generative Modeling of Molecular Dynamics Trajectories. CoRR Bowen Jing, Hannes Stärk, Tommi S. Jaakkola, Bonnie Berger
2024	B	`conf`	Secure Discovery of Genetic Relatives Across Large-Scale and Distributed Genomic Datasets. RECOMB Matthew M. Hong, David Froelicher, Ricky Magner, Victoria Popic, Bonnie Berger, Hyunghoon Cho
2023	J	`jnl`	Causally-guided Regularization of Graph Attention Improves Generalizability. Trans. Mach. Learn. Res. Alexander P. Wu, Thomas Markovich, Bonnie Berger, Nils Yannick Hammerla, Rohit Singh
2023	B	`conf`	Codon: A Compiler for High-Performance Pythonic Applications and DSLs. CC Ariya Shajii, Gabriel Ramirez, Haris Smajlovic, Jessica Ray, Bonnie Berger, Saman P. Amarasinghe, Ibrahim Numanagic
2023	J	`jnl`	EigenFold: Generative Protein Structure Prediction with Diffusion Models. CoRR Bowen Jing, Ezra Erives, Peter Pao-Huang, Gabriele Corso, Bonnie Berger, Tommi S. Jaakkola
2023	J	`jnl`	Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms. CoRR Bowen Jing, Tommi S. Jaakkola, Bonnie Berger
2023	A*	`conf`	Scalable and Privacy-Preserving Federated Principal Component Analysis. SP David Froelicher, Hyunghoon Cho, Manaswitha Edupalli, Joao Sa Sousa, Jean-Philippe Bossuat, Apostolos Pyrgelis, Juan Ramón Troncoso-Pastoriza, Bonnie Berger, Jean-Pierre Hubaux
2023	J	`jnl`	Scalable and Privacy-Preserving Federated Principal Component Analysis. CoRR David Froelicher, Hyunghoon Cho, Manaswitha Edupalli, Joao Sa Sousa, Jean-Philippe Bossuat, Apostolos Pyrgelis, Juan Ramón Troncoso-Pastoriza, Bonnie Berger, Jean-Pierre Hubaux
2023	J	`jnl`	TT3D: Leveraging precomputed protein 3D sequence models to predict protein-protein interactions. Bioinform. Samuel Sledzieski, Kapil Devkota, Rohit Singh, Lenore Cowen, Bonnie Berger
2023	J	`jnl`	sfkit: a web-based toolkit for secure and federated genomic analysis. Nucleic Acids Res. Simon Mendelsohn, David Froelicher, Denis Loginov, David Bernick, Bonnie Berger, Hyunghoon Cho
2023	J	`jnl`	virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2. J. Comput. Biol. Sumaira Zaman, Samuel Sledzieski, Bonnie Berger, Yi-Chieh Wu, Mukul S. Bansal
2022	J	`jnl`	Causally-guided Regularization of Graph Attention Improves Generalizability. CoRR Alexander P. Wu, Thomas Markovich, Bonnie Berger, Nils Hammerla, Rohit Singh
2022	A*	`conf`	Granger causal inference on DAGs identifies genomic loci regulating transcription. ICLR Alexander P. Wu, Rohit Singh, Bonnie Berger
2022	J	`jnl`	Granger causal inference on DAGs identifies genomic loci regulating transcription. CoRR Rohit Singh, Alexander P. Wu, Bonnie Berger
2022	—	`conf`	Sequre: a high-performance framework for rapid development of secure bioinformatics pipelines. IPDPS Workshops Haris Smajlovic, Ariya Shajii, Bonnie Berger, Hyunghoon Cho, Ibrahim Numanagic
2022	J	`jnl`	Topsy-Turvy: integrating a global view into sequence-based PPI prediction. Bioinform. Rohit Singh, Kapil Devkota, Samuel Sledzieski, Bonnie Berger, Lenore Cowen
2021	J	`jnl`	Bayesian information sharing enhances detection of regulatory associations in rare cell types. Bioinform. Alexander P. Wu, Jian Peng, Bonnie Berger, Hyunghoon Cho
2021	A*	`conf`	CryoDRGN2: Ab initio neural reconstruction of 3D protein structures from real cryo-EM images. ICCV Ellen D. Zhong, Adam Lerer, Joseph H. Davis, Bonnie Berger
2021	J	`jnl`	Levenshtein Distance, Sequence Comparison and Biological Database Search. IEEE Trans. Inf. Theory Bonnie Berger, Michael S. Waterman, Yun William Yu
2021	A*	`conf`	Multi-resolution modeling of a discrete stochastic process identifies causes of cancer. ICLR Adam Uri Yaari, Maxwell Sherman, Oliver Clarke Priebe, Po-Ru Loh, Boris Katz, Andrei Barbu, Bonnie Berger
2020	B	`conf`	A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets. RECOMB Baris Ekim, Bonnie Berger, Yaron Orenstein
2020	J	`jnl`	Hopper: a mathematically optimal algorithm for sketching biological data. Bioinform. Benjamin Demeo, Bonnie Berger
2020	A*	`conf`	Learning Mutational Semantics. NeurIPS Brian Hie, Ellen D. Zhong, Bryan Bryson, Bonnie Berger
2020	J	`jnl`	Meta-analysis of Caenorhabditis elegans single-cell developmental data reveals multi-frequency oscillation in gene activation. Bioinform. Luke A. D. Hutchison, Bonnie Berger, Isaac S. Kohane
2020	B	`conf`	Privacy-Preserving Biomedical Database Queries with Optimal Privacy-Utility Trade-Offs. RECOMB Hyunghoon Cho, Sean Simmons, Ryan Kim, Bonnie Berger
2020	A*	`conf`	Reconstructing continuous distributions of 3D protein structure from cryo-EM images. ICLR Ellen D. Zhong, Tristan Bepler, Joseph H. Davis, Bonnie Berger
2020	J	`jnl`	scVAE: variational auto-encoders for single-cell gene expression data. Bioinform. Christopher Heje Grønbech, Maximillian Fornitz Vording, Pascal N. Timshel, Casper Kaae Sønderby, Tune H. Pers, Ole Winther, Bonnie Berger
2019	A*	`conf`	Explicitly disentangling image content from translation and rotation with spatial-VAE. NeurIPS Tristan Bepler, Ellen D. Zhong, Kotaro Kelley, Edward Brignole, Bonnie Berger
2019	J	`jnl`	Explicitly disentangling image content from translation and rotation with spatial-VAE. CoRR Tristan Bepler, Ellen D. Zhong, Kotaro Kelley, Edward Brignole, Bonnie Berger
2019	B	`conf`	Geometric Sketching of Single-Cell Data Preserves Transcriptional Structure. RECOMB Brian Hie, Hyunghoon Cho, Benjamin Demeo, Bryan Bryson, Bonnie Berger
2019	A	`conf`	Large-Margin Classification in Hyperbolic Space. AISTATS Hyunghoon Cho, Benjamin Demeo, Jian Peng, Bonnie Berger
2019	—	`conf`	Learning protein sequence embeddings using information from structure. ICLR (Poster) Tristan Bepler, Bonnie Berger
2019	J	`jnl`	Learning protein sequence embeddings using information from structure. CoRR Tristan Bepler, Bonnie Berger
2019	J	`jnl`	Metagenomic binning through low-density hashing. Bioinform. Yunan Luo, Yun William Yu, Jianyang Zeng, Bonnie Berger, Jian Peng
2019	Misc	`conf`	Protecting Genomic Data Privacy with Probabilistic Modeling. PSB Sean Simmons, Bonnie Berger, S. Cenk Sahinalp
2019	J	`jnl`	Reconstructing continuously heterogeneous structures from single particle cryo-EM with deep generative models. CoRR Ellen D. Zhong, Tristan Bepler, Joseph H. Davis, Bonnie Berger
2019	J	`jnl`	Seq: a high-performance language for bioinformatics. Proc. ACM Program. Lang. Ariya Shajii, Ibrahim Numanagic, Riyadh Baghdadi, Bonnie Berger, Saman P. Amarasinghe
2018	C	`conf`	A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models. WABI Hooman Zabeti, Tamon Stephen, Bonnie Berger, Leonid Chindelevitch
2018	J	`jnl`	Fast Characterization of Segmental Duplications in Genome Assemblies. CoRR Ibrahim Numanagic, Alim S. Gökkaya, Lillian Zhang, Bonnie Berger, Can Alkan, Faraz Hach
2018	J	`jnl`	Fast characterization of segmental duplications in genome assemblies. Bioinform. Ibrahim Numanagic, Alim S. Gökkaya, Lillian Zhang, Bonnie Berger, Can Alkan, Faraz Hach
2018	B	`conf`	Generalizable Visualization of Mega-Scale Single-Cell Data. RECOMB Hyunghoon Cho, Bonnie Berger, Jian Peng
2018	J	`jnl`	Joker de Bruijn: Covering J. Comput. Biol. Yaron Orenstein, Yun William Yu, Bonnie Berger
2018	J	`jnl`	Large-Margin Classification in Hyperbolic Space. CoRR Hyunghoon Cho, Benjamin Demeo, Jian Peng, Bonnie Berger
2018	B	`conf`	Latent Variable Model for Aligning Barcoded Short-Reads Improves Downstream Analyses. RECOMB Ariya Shajii, Ibrahim Numanagic, Bonnie Berger
2018	B	`conf`	Positive-Unlabeled Convolutional Neural Networks for Particle Picking in Cryo-electron Micrographs. RECOMB Tristan Bepler, Andrew Morin, Alex J. Noble, Julia Brasch, Lawrence Shapiro, Bonnie Berger
2018	J	`jnl`	Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. CoRR Tristan Bepler, Andrew Morin, Alex J. Noble, Julia Brasch, Lawrence Shapiro, Bonnie Berger
2017	J	`jnl`	2017 ISCB Accomplishment by a Senior Scientist Award given to Pavel Pevzner. PLoS Comput. Biol. Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
2017	J	`jnl`	2017 ISCB Accomplishment by a Senior Scientist Award: Pavel Pevzner. F1000Research Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
2017	J	`jnl`	2017 ISCB Innovator Award: Aviv Regev. F1000Research Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
2017	J	`jnl`	2017 ISCB Innovator Award: Aviv Regev. PLoS Comput. Biol. Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
2017	J	`jnl`	2017 ISCB Overton Prize awarded to Christoph Bock. PLoS Comput. Biol. Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
2017	J	`jnl`	2017 ISCB Overton Prize: Christoph Bock. F1000Research Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
2017	J	`jnl`	2017 Outstanding Contributions to ISCB Award: Fran Lewitter. F1000Research Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
2017	J	`jnl`	2017 Outstanding Contributions to ISCB Award: Fran Lewitter. PLoS Comput. Biol. Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
2017	J	`jnl`	ISCB's initial reaction to New England Journal of Medicine editorial on data sharing. Bioinform. Bonnie Berger, Terry Gaasterland, Thomas Lengauer, Christine A. Orengo, Bruno Gaëta, Scott Markel, Alfonso Valencia
2017	J	`jnl`	Identification of protein complexes by integrating multiple alignment of protein interaction networks. Bioinform. Cheng-Yu Ma, Yi-Ping Phoebe Chen, Bonnie Berger, Chung-Shou Liao
2017	B	`conf`	Joker de Bruijn: Sequence Libraries to Cover All k-mers Using Joker Characters. RECOMB Yaron Orenstein, Ryan Kim, Polly Fordyce, Bonnie Berger
2017	J	`jnl`	Message from the ISCB: 2017 ISCB Accomplishment by a Senior Scientist Award Given to Pavel Pevzner. Bioinform. Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
2017	J	`jnl`	Message from the ISCB: 2017 ISCB Innovator Award Given to Aviv Regev. Bioinform. Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
2017	J	`jnl`	Message from the ISCB: 2017 ISCB Overton Prize Awarded to Christoph Bock. Bioinform. Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
2017	J	`jnl`	Message from the ISCB: 2017 Outstanding Contributions to ISCB Award Given to Fran Lewitter. Bioinform. Christiana N. Fogg, Diane E. Kovats, Bonnie Berger
2016	B	`conf`	An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values. DCC Claudio Alberti, Noah M. Daniels, Mikel Hernaez, Jan Voges, Rachel L. Goldfeder, Ana A. Hernandez-Lopez, Marco Mattavelli, Bonnie Berger
2016	J	`jnl`	Computational biology in the 21st century: scaling with compressive algorithms. Commun. ACM Bonnie Berger, Noah M. Daniels
2016	J	`jnl`	Efficient Design of Compact Unstructured RNA Libraries Covering All J. Comput. Biol. Yaron Orenstein, Bonnie Berger
2016	B	`conf`	Enabling Privacy Preserving GWAS in Heterogeneous Human Populations. RECOMB Sean Simmons, S. Cenk Sahinalp, Bonnie Berger
2016	J	`jnl`	Fast genotyping of known SNPs through approximate Bioinform. Ariya Shajii, Deniz Yörükoglu, Yun William Yu, Bonnie Berger
2016	J	`jnl`	ISCB's Initial Reaction to PLoS Comput. Biol. Bonnie Berger, Terry Gaasterland, Thomas Lengauer, Christine A. Orengo, Bruno Gaëta, Scott Markel, Alfonso Valencia
2016	B	`conf`	Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning. RECOMB Yunan Luo, Jianyang Zeng, Bonnie Berger, Jian Peng
2016	J	`jnl`	RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data. Bioinform. Yaron Orenstein, Yuhao Wang, Bonnie Berger
2016	J	`jnl`	Realizing privacy preserving genome-wide association studies. Bioinform. Sean Simmons, Bonnie Berger
2015	B	`conf`	Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks. RECOMB Hyunghoon Cho, Bonnie Berger, Jian Peng
2015	J	`jnl`	Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks. CoRR Hyunghoon Cho, Bonnie Berger, Jian Peng
2015	J	`jnl`	Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data. J. Comput. Biol. Sean Simmons, Jian Peng, Jadwiga R. Bienkowska, Bonnie Berger
2015	C	`conf`	Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers. WABI Yaron Orenstein, Bonnie Berger
2015	J	`jnl`	Entropy-scaling search of massive biological data. CoRR Yun William Yu, Noah M. Daniels, David Christian Danko, Bonnie Berger
2015	J	`jnl`	Exploiting ontology graph for predicting sparsely annotated gene function. Bioinform. Sheng Wang, Hyunghoon Cho, ChengXiang Zhai, Bonnie Berger, Jian Peng
2015	B	`conf`	HapTree-X: An Integrative Bayesian Framework for Haplotype Reconstruction from Transcriptome and Genome Sequencing Data. RECOMB Emily Berger, Deniz Yörükoglu, Bonnie Berger
2015	J	`jnl`	ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus. PLoS Comput. Biol. Peter D. Karp, Bonnie Berger, Diane E. Kovats, Thomas Lengauer, Michal Linial, Pardis Sabeti, Winston Hide, Burkhard Rost
2015	J	`jnl`	Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus. Bioinform. Peter D. Karp, Bonnie Berger, Diane E. Kovats, Thomas Lengauer, Michal Linial, Pardis Sabeti, Winston Hide, Burkhard Rost
2015	—	`conf`	One Size Doesn't Fit All: Measuring Individual Privacy in Aggregate Genomic Data. IEEE Symposium on Security and Privacy Workshops Sean Simmons, Bonnie Berger
2014	B	`conf`	HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data. RECOMB Emily Berger, Deniz Yörükoglu, Jian Peng, Bonnie Berger
2014	J	`jnl`	HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data. PLoS Comput. Biol. Emily Berger, Deniz Yörükoglu, Jian Peng, Bonnie Berger
2014	J	`jnl`	Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. BMC Syst. Biol. 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
2014	J	`jnl`	Simultaneous Alignment and Folding of Protein Sequences. J. Comput. Biol. Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger
2014	B	`conf`	Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification. RECOMB Yun William Yu, Deniz Yörükoglu, Bonnie Berger
2013	J	`jnl`	A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis. BMC Bioinform. George Tucker, Po-Ru Loh, Bonnie Berger
2013	J	`jnl`	Compressive genomics for protein databases. Bioinform. Noah M. Daniels, Andrew Gallant, Jian Peng, Lenore J. Cowen, Michael Baym, Bonnie Berger
2013	J	`jnl`	Optimizing a global alignment of protein interaction networks. Bioinform. Leonid Chindelevitch, Cheng-Yu Ma, Chung-Shou Liao, Bonnie Berger
2013	J	`jnl`	Reconstruction of phyletic trees by global alignment of multiple metabolic networks. BMC Bioinform. Cheng-Yu Ma, Shu-Hsi Lin, Chi-Ching Lee, Chuan Yi Tang, Bonnie Berger, Chung-Shou Liao
2012	J	`jnl`	Assessing statistical significance in causal graphs. BMC Bioinform. Leonid Chindelevitch, Po-Ru Loh, Ahmed Enayetallah, Bonnie Berger, Daniel Ziemek
2012	J	`jnl`	Editorial. Bioinform. Bonnie Berger
2012	J	`jnl`	Making sense out of massive data by going beyond differential expression. Proc. Natl. Acad. Sci. USA Patrick R. Schmid, Nathan P. Palmer, Isaac S. Kohane, Bonnie Berger
2012	J	`jnl`	SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone. Bioinform. Noah M. Daniels, Raghavendra Hosur, Bonnie Berger, Lenore J. Cowen
2012	B	`conf`	Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAs. RECOMB Sebastian Will, Michael Yu, Bonnie Berger
2011	J	`jnl`	A method for probing the mutational landscape of amyloid structure. Bioinform. Charles W. O'Donnell, Jérôme Waldispühl, Mieszko Lis, Randal Halfmann, Srinivas Devadas, Susan Lindquist, Bonnie Berger
2011	J	`jnl`	An Integrative Approach to Ortholog Prediction for Disease-Focused and Other Functional Studies. BMC Bioinform. Yanhui Hu, Ian Flockhart, Arunachalam Vinayagam, Clemens Bergwitz, Bonnie Berger, Norbert Perrimon, Stephanie E. Mohr
2011	B	`conf`	Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models. RECOMB Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger, Jérôme Waldispühl
2011	J	`jnl`	Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models. J. Comput. Biol. Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger, Jérôme Waldispühl
2011	J	`jnl`	IsoBase: a database of functionally related proteins across PPI networks. Nucleic Acids Res. Daniel Park, Rohit Singh, Michael Baym, Chung-Shou Liao, Bonnie Berger
2011	B	`conf`	Metabolic Network Analysis Demystified. RECOMB Leonid Chindelevitch, Aviv Regev, Bonnie Berger
2011	J	`jnl`	Preface: 14 J. Comput. Biol. Bonnie Berger
2011	J	`jnl`	Sparse estimation for structural variability. Algorithms Mol. Biol. Raghavendra Hosur, Rohit Singh, Bonnie Berger
2010	Misc	`conf`	Local Optimization for Global Alignment of Protein Interaction Networks. Pacific Symposium on Biocomputing Leonid Chindelevitch, Chung-Shou Liao, Bonnie Berger
2010	J	`jnl`	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 Matthew Menke, Bonnie Berger, Lenore Cowen
2010	B	`ed.`	Research in Computational Molecular Biology, 14th Annual International Conference, RECOMB 2010, Lisbon, Portugal, April 25-28, 2010. Proceedings RECOMB Bonnie Berger
2010	C	`conf`	Sparse Estimation for Structural Variability. WABI Raghavendra Hosur, Rohit Singh, Bonnie Berger
2010	J	`jnl`	Struct2Net: a web service to predict protein-protein interactions using a structure-based approach. Nucleic Acids Res. Rohit Singh, Daniel Park, Jinbo Xu, Raghavendra Hosur, Bonnie Berger
2009	J	`jnl`	BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis. PLoS Comput. Biol. Allen W. Bryan Jr., Matthew Menke, Lenore J. Cowen, Susan Lindquist, Bonnie Berger
2009	J	`jnl`	IsoRankN: spectral methods for global alignment of multiple protein networks. Bioinform. Chung-Shou Liao, Kanghao Lu, Michael Baym, Rohit Singh, Bonnie Berger
2009	J	`jnl`	RNAmutants: a web server to explore the mutational landscape of RNA secondary structures. Nucleic Acids Res. Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote
2009	B	`conf`	Simultaneous Alignment and Folding of Protein Sequences. RECOMB Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger
2008	J	`jnl`	Efficient Algorithms for Probing the RNA Mutation Landscape. PLoS Comput. Biol. Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote
2008	Misc	`conf`	Global Alignment of Multiple Protein Interaction Networks. Pacific Symposium on Biocomputing Rohit Singh, Jinbo Xu, Bonnie Berger
2008	J	`jnl`	Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc. Natl. Acad. Sci. USA Rohit Singh, Jinbo Xu, Bonnie Berger
2008	A*	`conf`	Graph algorithms for biological systems analysis. SODA Bonnie Berger, Rohit Singh, Jinbo Xu
2008	B	`conf`	High-Resolution Modeling of Cellular Signaling Networks. RECOMB Michael Baym, Chris Bakal, Norbert Perrimon, Bonnie Berger
2008	A*	`conf`	Inverting the Viterbi algorithm: an abstract framework for structure design. ICML Michael Schnall-Levin, Leonid Chindelevitch, Bonnie Berger
2008	J	`jnl`	Matt: Local Flexibility Aids Protein Multiple Structure Alignment. PLoS Comput. Biol. Matthew Menke, Bonnie Berger, Lenore Cowen
2008	J	`jnl`	Optimal contact map alignment of protein-protein interfaces. Bioinform. Vinay Pulim, Bonnie Berger, Jadwiga R. Bienkowska
2007	J	`jnl`	A Parameterized Algorithm for Protein Structure Alignment. J. Comput. Biol. Jinbo Xu, Feng Jiao, Bonnie Berger
2007	J	`jnl`	Automated real time constant-specificity surveillance for disease outbreaks. BMC Medical Informatics Decis. Mak. Shannon C. Wieland, John S. Brownstein, Bonnie Berger, Kenneth D. Mandl
2007	Misc	`conf`	Lthreader: Prediction of Ligand-Receptor Interactions Using Localized Threading. Pacific Symposium on Biocomputing Vinay Pulim, Jadwiga R. Bienkowska, Bonnie Berger
2007	B	`conf`	Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology. RECOMB Rohit Singh, Jinbo Xu, Bonnie Berger
2007	J	`jnl`	Predicting and Annotating Catalytic Residues: An Information Theoretic Approach. J. Comput. Biol. Beckett W. Sterner, Rohit Singh, Bonnie Berger
2007	Misc	`conf`	Probabilistic Modeling of Systematic Errors in Two-Hybrid Experiments. Pacific Symposium on Biocomputing David A. Sontag, Rohit Singh, Bonnie Berger
2006	B	`conf`	A Parameterized Algorithm for Protein Structure Alignment. RECOMB Jinbo Xu, Feng Jiao, Bonnie Berger
2006	J	`jnl`	Fast and accurate algorithms for protein side-chain packing. J. ACM Jinbo Xu, Bonnie Berger
2006	J	`jnl`	Paircoil2: improved prediction of coiled coils from sequence. Bioinform. A. V. McDonnell, Taijiao Jiang, Amy E. Keating, Bonnie Berger
2006	Misc	`conf`	Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction. Pacific Symposium on Biocomputing Rohit Singh, Jinbo Xu, Bonnie Berger
2006	J	`jnl`	transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels. Nucleic Acids Res. Jérôme Waldispühl, Bonnie Berger, Peter Clote, Jean-Marc Steyaert
2005	—	`conf`	A Tree-Decomposition Approach to Protein Structure Prediction. CSB Jinbo Xu, Feng Jiao, Bonnie Berger
2005	A*	`conf`	Active learning for sampling in time-series experiments with application to gene expression analysis. ICML Rohit Singh, Nathan P. Palmer, David K. Gifford, Bonnie Berger, Ziv Bar-Joseph
2005	Misc	`conf`	ChainTweak: Sampling from the Neighbourhood of a Protein Conformation. Pacific Symposium on Biocomputing Rohit Singh, Bonnie Berger
2005	J	`jnl`	Wrap-and-Pack: A New Paradigm for Beta Structural Motif Recognition with Application to Recognizing Beta Trefoils. J. Comput. Biol. Matthew Menke, Jonathan King, Bonnie Berger, Lenore Cowen
2004	J	`jnl`	Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery. J. Comput. Biol. Manolis Kellis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric S. Lander
2004	B	`conf`	Wrap-and-pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils. RECOMB Matthew Menke, Eben Scanlon, Jonathan King, Bonnie Berger, Lenore Cowen
2004	J	`jnl`	msari. Proc. Natl. Acad. Sci. USA Alex Coventry, Daniel J. Kleitman, Bonnie Berger
2003	B	`conf`	Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species. RECOMB Manolis Kamvysselis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric S. Lander
2002	J	`jnl`	Predicting the Beta-Helix Fold from Protein Sequence Data. J. Comput. Biol. Lenore Cowen, Phil Bradley, Matthew Menke, Jonathan King, Bonnie Berger
2002	B	`conf`	Trilogy: discovery of sequence-structure patterns across diverse proteins. RECOMB Phil Bradley, Peter S. Kim, Bonnie Berger
2001	B	`conf`	Predicting the beta-helix fold from protein sequence data. RECOMB Phil Bradley, Lenore Cowen, Matthew Menke, Jonathan King, Bonnie Berger
2000	B	`conf`	Human and mouse gene structure: comparative analysis and application to exon prediction. RECOMB Serafim Batzoglou, Lior Pachter, Jill P. Mesirov, Bonnie Berger, Eric S. Lander
2000	J	`jnl`	Local rule mechanism for selecting icosahedral shell geometry. Discret. Appl. Math. Bonnie Berger, Jonathan A. King, Russell Schwartz, Peter W. Shor
2000	B	`conf`	Sequencing a genome by walking with clone-end sequences: a mathematical analysis (abstract). RECOMB Serafim Batzoglou, Bonnie Berger, Jill P. Mesirov, Eric S. Lander
1999	J	`jnl`	A Dictionary-Based Approach for Gene Annotation. J. Comput. Biol. Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, Eric Banks, Eric S. Lander, Daniel J. Kleitman, Bonnie Berger
1999	B	`conf`	A dictionary based approach for gene annotation. RECOMB Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, William S. Beebee, Eric S. Lander, Bonnie Berger, Daniel J. Kleitman
1999	J	`jnl`	On the Structure of the Scaffolding Core of Bacteriophage T4. J. Comput. Biol. Bonnie Berger, G. W. Hoest, J. R. Paulson, Peter W. Shor
1999	J	`jnl`	Reconstructing a Three-Dimensional Model with Arbitrary Errors. J. ACM Bonnie Berger, Jon M. Kleinberg, Frank Thomson Leighton
1998	J	`jnl`	Computational learning reveals coiled coil-like motifs in histidine kinase linker domains. Proc. Natl. Acad. Sci. USA Mona Singh, Bonnie Berger, Peter S. Kim, James M. Berger, Andrea G. Cochran
1998	J	`jnl`	Near-Linear Time Construction of Sparse Neighborhood Covers. SIAM J. Comput. Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg
1998	J	`jnl`	Protein Folding in the Hydrophobic-Hydrophilic(HP) Model is NP-Complete. J. Comput. Biol. Bonnie Berger, Frank Thomson Leighton
1998	B	`conf`	Protein folding in the hydrophobic-hydrophilic ( RECOMB Bonnie Berger, Frank Thomson Leighton
1997	J	`jnl`	An Iterative Method for Improved Protein Structural Motif Recognition. J. Comput. Biol. Bonnie Berger, Mona Singh
1997	B	`conf`	An iterative method for improved protein structural motif recognition. RECOMB Bonnie Berger, Mona Singh
1997	J	`jnl`	The Fourth Moment Method. SIAM J. Comput. Bonnie Berger
1997	J	`jnl`	Tight Bounds for the Maximum Acyclic Subgraph Problem. J. Algorithms Bonnie Berger, Peter W. Shor
1996	J	`jnl`	Fast Distributed Network Decompositions and Covers. J. Parallel Distributed Comput. Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg
1996	A*	`conf`	Reconstructing a Three-Dimensional Model with Arbitrary Errors. STOC Bonnie Berger, Jon M. Kleinberg, Frank Thomson Leighton
1995	J	`jnl`	Algorithms for Protein Structural Motif Recognition. J. Comput. Biol. Bonnie Berger
1995	A*	`conf`	Improved Algorithms for Protein Motif Recognition. SODA Bonnie Berger, David Bruce Wilson
1995	J	`jnl`	Nearly Optimal Algorithms and Bounds for Multilayer Channel Routing. J. ACM Bonnie Berger, Martin L. Brady, Donna J. Brown, Frank Thomson Leighton
1995	J	`jnl`	Scheduling with Concurrency-Based Constraints. J. Algorithms Bonnie Berger, Lenore Cowen
1994	J	`jnl`	Efficient NC Algorithms for Set Cover with Applications to Learning and Geometry. J. Comput. Syst. Sci. Bonnie Berger, John Rompel, Peter W. Shor
1994	J	`jnl`	Low-Diameter Graph Decomposition Is in NC. Random Struct. Algorithms Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg
1993	A*	`conf`	Near-Linear Cost Sequential and Distribured Constructions of Sparse Neighborhood Covers FOCS Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg
1992	A*	`conf`	Fast Network Decomposition (Extended Abstract). PODC Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg
1992	—	`conf`	Low-Diameter Graph Decomposition is in NC. SWAT Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg
1991	A*	`conf`	Complexity Results and Algorithms for { <, <=, = }-Constrained Scheduling. SODA Bonnie Berger, Lenore Cowen
1991	J	`jnl`	Simulating (log c n)-Wise Independence in NC. J. ACM Bonnie Berger, John Rompel
1991	A*	`conf`	The Fourth Moment Method. SODA Bonnie Berger
1990	J	`jnl`	A Better Performance Guarantee for Approximate Graph Coloring. Algorithmica Bonnie Berger, John Rompel
1990	A*	`conf`	Approximation Algorithms for the Maximum Acyclic Subgraph Problem. SODA Bonnie Berger, Peter W. Shor
1989	A*	`conf`	Efficient NC Algorithms for Set Cover with Applications to Learning and Geometry FOCS Bonnie Berger, John Rompel, Peter W. Shor
1989	A*	`conf`	Simulating (log ^c n)-wise Independence in NC FOCS Bonnie Berger, John Rompel