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- affiliation: MIT, Cambridge, USA
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2020 – today
- 2025
[i21]Divya Shanmugam, Shuvom Sadhuka, Manish Raghavan, John V. Guttag, Bonnie Berger, Emma Pierson:
Evaluating multiple models using labeled and unlabeled data. CoRR abs/2501.11866 (2025)- 2024
- [c71]Bowen Jing, Tommi S. Jaakkola, Bonnie Berger:
Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms. ICLR 2024 - [c70]Bowen Jing, Bonnie Berger, Tommi S. Jaakkola:
AlphaFold Meets Flow Matching for Generating Protein Ensembles. ICML 2024 - [c69]Hannes Stärk, Bowen Jing, Chenyu Wang, Gabriele Corso, Bonnie Berger, Regina Barzilay, Tommi S. Jaakkola:
Dirichlet Flow Matching with Applications to DNA Sequence Design. ICML 2024 - [c68]Bowen Jing, Hannes Stärk, Tommi S. Jaakkola, Bonnie Berger:
Generative Modeling of Molecular Dynamics Trajectories. NeurIPS 2024 - [c67]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: 308-313 - [i20]Bowen Jing, Bonnie Berger, Tommi S. Jaakkola:
AlphaFold Meets Flow Matching for Generating Protein Ensembles. CoRR abs/2402.04845 (2024) - [i19]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 abs/2402.05841 (2024) - [i18]Bowen Jing, Hannes Stärk, Tommi S. Jaakkola, Bonnie Berger:
Generative Modeling of Molecular Dynamics Trajectories. CoRR abs/2409.17808 (2024) - 2023
- [j88]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) - [j87]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): 3-20 (2023) - [j86]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): 535-541 (2023) - [j85]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) - [c66]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: 191-202 - [c65]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: 1908-1925 - [i17]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 abs/2304.00129 (2023) - [i16]Bowen Jing, Ezra Erives, Peter Pao-Huang, Gabriele Corso, Bonnie Berger, Tommi S. Jaakkola:
EigenFold: Generative Protein Structure Prediction with Diffusion Models. CoRR abs/2304.02198 (2023) - [i15]Bowen Jing, Tommi S. Jaakkola, Bonnie Berger:
Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms. CoRR abs/2312.04323 (2023) - 2022
- [j84]Rohit Singh, Kapil Devkota, Samuel Sledzieski, Bonnie Berger, Lenore Cowen:
Topsy-Turvy: integrating a global view into sequence-based PPI prediction. Bioinform. 38(Supplement_1): i264-i272 (2022) - [c64]Alexander P. Wu, Rohit Singh, Bonnie Berger:
Granger causal inference on DAGs identifies genomic loci regulating transcription. ICLR 2022 - [c63]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: 164-165 - [i14]Rohit Singh, Alexander P. Wu, Bonnie Berger:
Granger causal inference on DAGs identifies genomic loci regulating transcription. CoRR abs/2210.10168 (2022) - [i13]Alexander P. Wu, Thomas Markovich, Bonnie Berger, Nils Hammerla, Rohit Singh:
Causally-guided Regularization of Graph Attention Improves Generalizability. CoRR abs/2210.10946 (2022) - 2021
- [j83]Alexander P. Wu, Jian Peng, Bonnie Berger, Hyunghoon Cho:
Bayesian information sharing enhances detection of regulatory associations in rare cell types. Bioinform. 37(Supplement): 349-357 (2021) - [j82]Bonnie Berger, Michael S. Waterman, Yun William Yu:
Levenshtein Distance, Sequence Comparison and Biological Database Search. IEEE Trans. Inf. Theory 67(6): 3287-3294 (2021) - [c62]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: 4046-4055 - [c61]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 - 2020
- [j81]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): 4047-4057 (2020) - [j80]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): 4415-4422 (2020) - [j79]Benjamin Demeo, Bonnie Berger:
Hopper: a mathematically optimal algorithm for sketching biological data. Bioinform. 36(Supplement-1): i236-i241 (2020) - [c60]Ellen D. Zhong, Tristan Bepler, Joseph H. Davis, Bonnie Berger:
Reconstructing continuous distributions of 3D protein structure from cryo-EM images. ICLR 2020 - [c59]Brian Hie, Ellen D. Zhong, Bryan Bryson, Bonnie Berger:
Learning Mutational Semantics. NeurIPS 2020 - [c58]Baris Ekim, Bonnie Berger, Yaron Orenstein:
A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets. RECOMB 2020: 37-53 - [c57]Hyunghoon Cho, Sean Simmons, Ryan Kim, Bonnie Berger:
Privacy-Preserving Biomedical Database Queries with Optimal Privacy-Utility Trade-Offs. RECOMB 2020: 245-247
2010 – 2019
- 2019
- [j78]Yunan Luo, Yun William Yu, Jianyang Zeng, Bonnie Berger, Jian Peng:
Metagenomic binning through low-density hashing. Bioinform. 35(2): 219-226 (2019) - [j77]Ariya Shajii, Ibrahim Numanagic, Riyadh Baghdadi, Bonnie Berger, Saman P. Amarasinghe:
Seq: a high-performance language for bioinformatics. Proc. ACM Program. Lang. 3(OOPSLA): 125:1-125:29 (2019) - [c56]Hyunghoon Cho, Benjamin Demeo, Jian Peng, Bonnie Berger:
Large-Margin Classification in Hyperbolic Space. AISTATS 2019: 1832-1840 - [c55]Tristan Bepler, Bonnie Berger:
Learning protein sequence embeddings using information from structure. ICLR (Poster) 2019 - [c54]Tristan Bepler, Ellen D. Zhong, Kotaro Kelley, Edward Brignole, Bonnie Berger:
Explicitly disentangling image content from translation and rotation with spatial-VAE. NeurIPS 2019: 15409-15419 - [c53]Sean Simmons, Bonnie Berger, S. Cenk Sahinalp:
Protecting Genomic Data Privacy with Probabilistic Modeling. PSB 2019: 403-414 - [c52]Brian Hie, Hyunghoon Cho, Benjamin Demeo, Bryan Bryson, Bonnie Berger:
Geometric Sketching of Single-Cell Data Preserves Transcriptional Structure. RECOMB 2019: 299-301 - [i12]Tristan Bepler, Bonnie Berger:
Learning protein sequence embeddings using information from structure. CoRR abs/1902.08661 (2019) - [i11]Ellen D. Zhong, Tristan Bepler, Joseph H. Davis, Bonnie Berger:
Reconstructing continuously heterogeneous structures from single particle cryo-EM with deep generative models. CoRR abs/1909.05215 (2019) - [i10]Tristan Bepler, Ellen D. Zhong, Kotaro Kelley, Edward Brignole, Bonnie Berger:
Explicitly disentangling image content from translation and rotation with spatial-VAE. CoRR abs/1909.11663 (2019) - 2018
- [j76]Ibrahim Numanagic, Alim S. Gökkaya, Lillian Zhang, Bonnie Berger, Can Alkan, Faraz Hach:
Fast characterization of segmental duplications in genome assemblies. Bioinform. 34(17): i706-i714 (2018) - [j75]Yaron Orenstein, Yun William Yu, Bonnie Berger:
Joker de Bruijn: Covering k-Mers Using Joker Characters. J. Comput. Biol. 25(11): 1171-1178 (2018) - [c51]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: 245-247 - [c50]Hyunghoon Cho, Bonnie Berger, Jian Peng:
Generalizable Visualization of Mega-Scale Single-Cell Data. RECOMB 2018: 251-253 - [c49]Ariya Shajii, Ibrahim Numanagic, Bonnie Berger:
Latent Variable Model for Aligning Barcoded Short-Reads Improves Downstream Analyses. RECOMB 2018: 280-282 - [c48]Hooman Zabeti, Tamon Stephen, Bonnie Berger, Leonid Chindelevitch:
A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models. WABI 2018: 1:1-1:13 - [i9]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 abs/1803.08207 (2018) - [i8]Hyunghoon Cho, Benjamin Demeo, Jian Peng, Bonnie Berger:
Large-Margin Classification in Hyperbolic Space. CoRR abs/1806.00437 (2018) - [i7]Ibrahim Numanagic, Alim S. Gökkaya, Lillian Zhang, Bonnie Berger, Can Alkan, Faraz Hach:
Fast Characterization of Segmental Duplications in Genome Assemblies. CoRR abs/1807.00205 (2018) - 2017
- [j74]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): 1681-1688 (2017) - [j73]Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
Message from the ISCB: 2017 ISCB Innovator Award Given to Aviv Regev. Bioinform. 33(14): 2243-2244 (2017) - [j72]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): 2245-2246 (2017) - [j71]Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
Message from the ISCB: 2017 ISCB Overton Prize Awarded to Christoph Bock. Bioinform. 33(14): 2247-2248 (2017) - [j70]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): 2249-2250 (2017) - [j69]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): 2968 (2017) - [j68]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) - [j67]Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
2017 Outstanding Contributions to ISCB Award: Fran Lewitter. PLoS Comput. Biol. 13(6) (2017) - [j66]Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
2017 ISCB Overton Prize awarded to Christoph Bock. PLoS Comput. Biol. 13(6) (2017) - [j65]Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
2017 ISCB Innovator Award: Aviv Regev. PLoS Comput. Biol. 13(6) (2017) - [c47]Yaron Orenstein, Ryan Kim, Polly Fordyce, Bonnie Berger:
Joker de Bruijn: Sequence Libraries to Cover All k-mers Using Joker Characters. RECOMB 2017: 389-390 - [i6]Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
2017 ISCB Innovator Award: Aviv Regev. F1000Research 6: 998- (2017) - [i5]Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
2017 ISCB Overton Prize: Christoph Bock. F1000Research 6: 999- (2017) - [i4]Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
2017 Outstanding Contributions to ISCB Award: Fran Lewitter. F1000Research 6: 1000- (2017) - [i3]Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
2017 ISCB Accomplishment by a Senior Scientist Award: Pavel Pevzner. F1000Research 6: 1001- (2017) - 2016
- [j64]Sean Simmons, Bonnie Berger:
Realizing privacy preserving genome-wide association studies. Bioinform. 32(9): 1293-1300 (2016) - [j63]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): 351-359 (2016) - [j62]Ariya Shajii, Deniz Yörükoglu, Yun William Yu, Bonnie Berger:
Fast genotyping of known SNPs through approximate k-mer matching. Bioinform. 32(17): 538-544 (2016) - [j61]Bonnie Berger, Noah M. Daniels:
Computational biology in the 21st century: scaling with compressive algorithms. Commun. ACM 59(8): 72-80 (2016) - [j60]Yaron Orenstein, Bonnie Berger:
Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers. J. Comput. Biol. 23(2): 67-79 (2016) - [j59]Bonnie Berger, Terry Gaasterland, Thomas Lengauer, Christine A. Orengo, Bruno Gaëta, Scott Markel, Alfonso Valencia:
ISCB's Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing. PLoS Comput. Biol. 12(3) (2016) - [c46]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: 221-230 - [c45]Sean Simmons, S. Cenk Sahinalp, Bonnie Berger:
Enabling Privacy Preserving GWAS in Heterogeneous Human Populations. RECOMB 2016: 246-247 - [c44]Yunan Luo, Jianyang Zeng, Bonnie Berger, Jian Peng:
Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning. RECOMB 2016: 255-257 - 2015
- [j58]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): 616-617 (2015) - [j57]Sheng Wang, Hyunghoon Cho, ChengXiang Zhai, Bonnie Berger, Jian Peng:
Exploiting ontology graph for predicting sparsely annotated gene function. Bioinform. 31(12): 357-364 (2015) - [j56]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): 715-728 (2015) - [j55]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) - [c43]Emily Berger, Deniz Yörükoglu, Bonnie Berger:
HapTree-X: An Integrative Bayesian Framework for Haplotype Reconstruction from Transcriptome and Genome Sequencing Data. RECOMB 2015: 28-29 - [c42]Hyunghoon Cho, Bonnie Berger, Jian Peng:
Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks. RECOMB 2015: 62-64 - [c41]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: 41-49 - [c40]Yaron Orenstein, Bonnie Berger:
Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers. WABI 2015: 308-325 - [i2]Yun William Yu, Noah M. Daniels, David Christian Danko, Bonnie Berger:
Entropy-scaling search of massive biological data. CoRR abs/1503.05638 (2015) - [i1]Hyunghoon Cho, Bonnie Berger, Jian Peng:
Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks. CoRR abs/1504.02719 (2015) - 2014
- [j54]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: 13 (2014) - [j53]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): 477-491 (2014) - [j52]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) - [c39]Emily Berger, Deniz Yörükoglu, Jian Peng, Bonnie Berger:
HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data. RECOMB 2014: 18-19 - [c38]Yun William Yu, Deniz Yörükoglu, Bonnie Berger:
Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification. RECOMB 2014: 385-399 - 2013
- [j51]Noah M. Daniels, Andrew Gallant, Jian Peng, Lenore J. Cowen, Michael Baym, Bonnie Berger:
Compressive genomics for protein databases. Bioinform. 29(13): 283-290 (2013) - [j50]Leonid Chindelevitch, Cheng-Yu Ma, Chung-Shou Liao, Bonnie Berger:
Optimizing a global alignment of protein interaction networks. Bioinform. 29(21): 2765-2773 (2013) - [j49]George Tucker, Po-Ru Loh, Bonnie Berger:
A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis. BMC Bioinform. 14: 299 (2013) - [j48]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): S12 (2013) - 2012
- [j47]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): 1216-1222 (2012) - [j46]Bonnie Berger:
Editorial. Bioinform. 28(12): 1 (2012) - [j45]Leonid Chindelevitch, Po-Ru Loh, Ahmed Enayetallah, Bonnie Berger, Daniel Ziemek:
Assessing statistical significance in causal graphs. BMC Bioinform. 13: 35 (2012) - [j44]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): 5594-5599 (2012) - [c37]Sebastian Will, Michael Yu, Bonnie Berger:
Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAs. RECOMB 2012: 341 - 2011
- [j43]Raghavendra Hosur, Rohit Singh, Bonnie Berger:
Sparse estimation for structural variability. Algorithms Mol. Biol. 6: 12 (2011) - [j42]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): 34-42 (2011) - [j41]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: 357 (2011) - [j40]Bonnie Berger:
Preface: 14th International Conference on Research in Computational Molecular Biology (RECOMB 2010). J. Comput. Biol. 18(3): 205 (2011) - [j39]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): 1635-1647 (2011) - [j38]Daniel Park, Rohit Singh, Michael Baym, Chung-Shou Liao, Bonnie Berger:
IsoBase: a database of functionally related proteins across PPI networks. Nucleic Acids Res. 39(Database-Issue): 295-300 (2011) - [c36]Leonid Chindelevitch, Aviv Regev, Bonnie Berger:
Metabolic Network Analysis Demystified. RECOMB 2011: 31-33 - [c35]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: 408-423 - 2010
- [j37]Rohit Singh, Daniel Park, Jinbo Xu, Raghavendra Hosur, Bonnie Berger:
Struct2Net: a web service to predict protein-protein interactions using a structure-based approach. Nucleic Acids Res. 38(Web-Server-Issue): 508-515 (2010) - [j36]Matthew Menke, Bonnie Berger, Lenore Cowen:
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 107(9): 4069-4074 (2010) - [c34]Leonid Chindelevitch, Chung-Shou Liao, Bonnie Berger:
Local Optimization for Global Alignment of Protein Interaction Networks. Pacific Symposium on Biocomputing 2010: 123-132 - [c33]Raghavendra Hosur, Rohit Singh, Bonnie Berger:
Sparse Estimation for Structural Variability. WABI 2010: 13-27 - [e1]Bonnie Berger:
Research in Computational Molecular Biology, 14th Annual International Conference, RECOMB 2010, Lisbon, Portugal, April 25-28, 2010. Proceedings. Lecture Notes in Computer Science 6044, Springer 2010, ISBN 978-3-642-12682-6 [contents]
2000 – 2009
- 2009
- [j35]Chung-Shou Liao, Kanghao Lu, Michael Baym, Rohit Singh, Bonnie Berger:
IsoRankN: spectral methods for global alignment of multiple protein networks. Bioinform. 25(12) (2009) - [j34]Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote:
RNAmutants: a web server to explore the mutational landscape of RNA secondary structures. Nucleic Acids Res. 37(Web-Server-Issue): 281-286 (2009) - [j33]Allen W. Bryan Jr., Matthew Menke, Lenore J. Cowen, Susan Lindquist, Bonnie Berger:
BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis. PLoS Comput. Biol. 5(3) (2009) - [c32]Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger:
Simultaneous Alignment and Folding of Protein Sequences. RECOMB 2009: 339-355 - 2008
- [j32]Vinay Pulim, Bonnie Berger, Jadwiga R. Bienkowska:
Optimal contact map alignment of protein-protein interfaces. Bioinform. 24(20): 2324-2328 (2008) - [j31]Matthew Menke, Bonnie Berger, Lenore Cowen:
Matt: Local Flexibility Aids Protein Multiple Structure Alignment. PLoS Comput. Biol. 4(1) (2008) - [j30]Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote:
Efficient Algorithms for Probing the RNA Mutation Landscape. PLoS Comput. Biol. 4(8) (2008) - [j29]Rohit Singh, Jinbo Xu, Bonnie Berger:
Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc. Natl. Acad. Sci. USA 105(35): 12763-12768 (2008) - [c31]Michael Schnall-Levin, Leonid Chindelevitch, Bonnie Berger:
Inverting the Viterbi algorithm: an abstract framework for structure design. ICML 2008: 904-911 - [c30]Rohit Singh, Jinbo Xu, Bonnie Berger:
Global Alignment of Multiple Protein Interaction Networks. Pacific Symposium on Biocomputing 2008: 303-314 - [c29]Michael Baym, Chris Bakal, Norbert Perrimon, Bonnie Berger:
High-Resolution Modeling of Cellular Signaling Networks. RECOMB 2008: 257-271 - [c28]Bonnie Berger, Rohit Singh, Jinbo Xu:
Graph algorithms for biological systems analysis. SODA 2008: 142-151 - 2007
- [j28]Jinbo Xu, Feng Jiao, Bonnie Berger:
A Parameterized Algorithm for Protein Structure Alignment. J. Comput. Biol. 14(5): 564-577 (2007) - [j27]Beckett W. Sterner, Rohit Singh, Bonnie Berger:
Predicting and Annotating Catalytic Residues: An Information Theoretic Approach. J. Comput. Biol. 14(8): 1058-1073 (2007) - [j26]Shannon C. Wieland, John S. Brownstein, Bonnie Berger, Kenneth D. Mandl:
Automated real time constant-specificity surveillance for disease outbreaks. BMC Medical Informatics Decis. Mak. 7: 15 (2007) - [c27]Vinay Pulim, Jadwiga R. Bienkowska, Bonnie Berger:
Lthreader: Prediction of Ligand-Receptor Interactions Using Localized Threading. Pacific Symposium on Biocomputing 2007: 64-75 - [c26]David A. Sontag, Rohit Singh, Bonnie Berger:
Probabilistic Modeling of Systematic Errors in Two-Hybrid Experiments. Pacific Symposium on Biocomputing 2007: 445-457 - [c25]Rohit Singh, Jinbo Xu, Bonnie Berger:
Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology. RECOMB 2007: 16-31 - 2006
- [j25]A. V. McDonnell, Taijiao Jiang, Amy E. Keating, Bonnie Berger:
Paircoil2: improved prediction of coiled coils from sequence. Bioinform. 22(3): 356-358 (2006) - [j24]Jinbo Xu, Bonnie Berger:
Fast and accurate algorithms for protein side-chain packing. J. ACM 53(4): 533-557 (2006) - [j23]Jérôme Waldispühl, Bonnie Berger, Peter Clote, Jean-Marc Steyaert:
transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels. Nucleic Acids Res. 34(Web-Server-Issue): 189-193 (2006) - [c24]Rohit Singh, Jinbo Xu, Bonnie Berger:
Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction. Pacific Symposium on Biocomputing 2006: 403-414 - [c23]Jinbo Xu, Feng Jiao, Bonnie Berger:
A Parameterized Algorithm for Protein Structure Alignment. RECOMB 2006: 488-499 - 2005
- [j22]Matthew Menke, Jonathan King, Bonnie Berger, Lenore Cowen:
Wrap-and-Pack: A New Paradigm for Beta Structural Motif Recognition with Application to Recognizing Beta Trefoils. J. Comput. Biol. 12(6): 777-795 (2005) - [c22]Jinbo Xu, Feng Jiao, Bonnie Berger:
A Tree-Decomposition Approach to Protein Structure Prediction. CSB 2005: 247-256 - [c21]Rohit Singh, Nathan P. Palmer, David K. Gifford, Bonnie Berger, Ziv Bar-Joseph:
Active learning for sampling in time-series experiments with application to gene expression analysis. ICML 2005: 832-839 - [c20]Rohit Singh, Bonnie Berger:
ChainTweak: Sampling from the Neighbourhood of a Protein Conformation. Pacific Symposium on Biocomputing 2005: 54-65 - 2004
- [j21]Manolis Kellis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric S. Lander:
Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery. J. Comput. Biol. 11(2/3): 319-355 (2004) - [j20]Alex Coventry, Daniel J. Kleitman, Bonnie Berger:
msari. Proc. Natl. Acad. Sci. USA 101(33): 12102-12107 (2004) - [c19]Matthew Menke, Eben Scanlon, Jonathan King, Bonnie Berger, Lenore Cowen:
Wrap-and-pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils. RECOMB 2004: 298-307 - 2003
- [c18]Manolis Kamvysselis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric S. Lander:
Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species. RECOMB 2003: 157-16 - 2002
- [j19]Lenore Cowen, Phil Bradley, Matthew Menke, Jonathan King, Bonnie Berger:
Predicting the Beta-Helix Fold from Protein Sequence Data. J. Comput. Biol. 9(2): 261-276 (2002) - [c17]Phil Bradley, Peter S. Kim, Bonnie Berger:
Trilogy: discovery of sequence-structure patterns across diverse proteins. RECOMB 2002: 77-88 - 2001
- [c16]Phil Bradley, Lenore Cowen, Matthew Menke, Jonathan King, Bonnie Berger:
Predicting the beta-helix fold from protein sequence data. RECOMB 2001: 59-67 - 2000
- [j18]Bonnie Berger, Jonathan A. King, Russell Schwartz, Peter W. Shor:
Local rule mechanism for selecting icosahedral shell geometry. Discret. Appl. Math. 104(1-3): 97-111 (2000) - [c15]Serafim Batzoglou, Bonnie Berger, Jill P. Mesirov, Eric S. Lander:
Sequencing a genome by walking with clone-end sequences: a mathematical analysis (abstract). RECOMB 2000: 45 - [c14]Serafim Batzoglou, Lior Pachter, Jill P. Mesirov, Bonnie Berger, Eric S. Lander:
Human and mouse gene structure: comparative analysis and application to exon prediction. RECOMB 2000: 46-53
1990 – 1999
- 1999
- [j17]Bonnie Berger, Jon M. Kleinberg, Frank Thomson Leighton:
Reconstructing a Three-Dimensional Model with Arbitrary Errors. J. ACM 46(2): 212-235 (1999) - [j16]Bonnie Berger, G. W. Hoest, J. R. Paulson, Peter W. Shor:
On the Structure of the Scaffolding Core of Bacteriophage T4. J. Comput. Biol. 6(1): 1-12 (1999) - [j15]Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, Eric Banks, Eric S. Lander, Daniel J. Kleitman, Bonnie Berger:
A Dictionary-Based Approach for Gene Annotation. J. Comput. Biol. 6(3/4): 419-430 (1999) - [c13]Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, William S. Beebee, Eric S. Lander, Bonnie Berger, Daniel J. Kleitman:
A dictionary based approach for gene annotation. RECOMB 1999: 285-294 - 1998
- [j14]Bonnie Berger, Frank Thomson Leighton:
Protein Folding in the Hydrophobic-Hydrophilic(HP) Model is NP-Complete. J. Comput. Biol. 5(1): 27-40 (1998) - [j13]Mona Singh, Bonnie Berger, Peter S. Kim, James M. Berger, Andrea G. Cochran:
Computational learning reveals coiled coil-like motifs in histidine kinase linker domains. Proc. Natl. Acad. Sci. USA 95(6): 2738-2743 (1998) - [j12]Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg:
Near-Linear Time Construction of Sparse Neighborhood Covers. SIAM J. Comput. 28(1): 263-277 (1998) - [c12]Bonnie Berger, Frank Thomson Leighton:
Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete. RECOMB 1998: 30-39 - 1997
- [j11]Bonnie Berger, Peter W. Shor:
Tight Bounds for the Maximum Acyclic Subgraph Problem. J. Algorithms 25(1): 1-18 (1997) - [j10]Bonnie Berger, Mona Singh:
An Iterative Method for Improved Protein Structural Motif Recognition. J. Comput. Biol. 4(3): 261-273 (1997) - [j9]Bonnie Berger:
The Fourth Moment Method. SIAM J. Comput. 26(4): 1188-1207 (1997) - [c11]Bonnie Berger, Mona Singh:
An iterative method for improved protein structural motif recognition. RECOMB 1997: 37-46 - 1996
- [j8]Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg:
Fast Distributed Network Decompositions and Covers. J. Parallel Distributed Comput. 39(2): 105-114 (1996) - [c10]Bonnie Berger, Jon M. Kleinberg, Frank Thomson Leighton:
Reconstructing a Three-Dimensional Model with Arbitrary Errors. STOC 1996: 449-458 - 1995
- [j7]Bonnie Berger, Martin L. Brady, Donna J. Brown, Frank Thomson Leighton:
Nearly Optimal Algorithms and Bounds for Multilayer Channel Routing. J. ACM 42(2): 500-542 (1995) - [j6]Bonnie Berger, Lenore Cowen:
Scheduling with Concurrency-Based Constraints. J. Algorithms 18(1): 98-123 (1995) - [j5]Bonnie Berger:
Algorithms for Protein Structural Motif Recognition. J. Comput. Biol. 2(1): 125-138 (1995) - [c9]Bonnie Berger, David Bruce Wilson:
Improved Algorithms for Protein Motif Recognition. SODA 1995: 58-67 - 1994
- [j4]Bonnie Berger, John Rompel, Peter W. Shor:
Efficient NC Algorithms for Set Cover with Applications to Learning and Geometry. J. Comput. Syst. Sci. 49(3): 454-477 (1994) - [j3]Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg:
Low-Diameter Graph Decomposition Is in NC. Random Struct. Algorithms 5(3): 441-452 (1994) - 1993
- [c8]Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg:
Near-Linear Cost Sequential and Distribured Constructions of Sparse Neighborhood Covers. FOCS 1993: 638-647 - 1992
- [c7]Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg:
Fast Network Decomposition (Extended Abstract). PODC 1992: 169-177 - [c6]Baruch Awerbuch, Bonnie Berger, Lenore Cowen, David Peleg:
Low-Diameter Graph Decomposition is in NC. SWAT 1992: 83-93 - 1991
- [j2]Bonnie Berger, John Rompel:
Simulating (log c n)-Wise Independence in NC. J. ACM 38(4): 1026-1046 (1991) - [c5]Bonnie Berger, Lenore Cowen:
Complexity Results and Algorithms for { <, <=, = }-Constrained Scheduling. SODA 1991: 137-147 - [c4]Bonnie Berger:
The Fourth Moment Method. SODA 1991: 373-383 - 1990
- [j1]Bonnie Berger, John Rompel:
A Better Performance Guarantee for Approximate Graph Coloring. Algorithmica 5(3): 459-466 (1990) - [c3]Bonnie Berger, Peter W. Shor:
Approximation Algorithms for the Maximum Acyclic Subgraph Problem. SODA 1990: 236-243
1980 – 1989
- 1989
- [c2]Bonnie Berger, John Rompel:
Simulating (log ^c n)-wise Independence in NC. FOCS 1989: 2-7 - [c1]Bonnie Berger, John Rompel, Peter W. Shor:
Efficient NC Algorithms for Set Cover with Applications to Learning and Geometry. FOCS 1989: 54-59
Coauthor Index
Lenore Cowen
aka: Lenore J. Cowen
aka: Lenore J. Cowen
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