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Bonnie Berger - Publications

Affiliations: 
1992- Mathematics Massachusetts Institute of Technology, Cambridge, MA, United States 
Area:
Theoretical Computer Science, Computational Biological Modeling, Computational Biology
Website:
https://math.mit.edu/directory/profile.html?pid=20
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114 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Sledzieski S, Devkota K, Singh R, Cowen L, Berger B. TT3D: Leveraging Pre-Computed Protein 3D Sequence Models to Predict Protein-Protein Interactions. Bioinformatics (Oxford, England). PMID 37897686 DOI: 10.1093/bioinformatics/btad663  0.554
2023 Pellow D, Pu L, Ekim B, Kotlar L, Berger B, Shamir R, Orenstein Y. Efficient minimizer orders for large values of using minimum decycling sets. Genome Research. PMID 37558282 DOI: 10.1101/gr.277644.123  0.758
2023 Ekim B, Sahlin K, Medvedev P, Berger B, Chikhi R. Efficient mapping of accurate long reads in minimizer space with mapquik. Genome Research. PMID 37399256 DOI: 10.1101/gr.277679.123  0.774
2023 Singh R, Sledzieski S, Bryson B, Cowen L, Berger B. Contrastive learning in protein language space predicts interactions between drugs and protein targets. Proceedings of the National Academy of Sciences of the United States of America. 120: e2220778120. PMID 37289807 DOI: 10.1073/pnas.2220778120  0.527
2023 Kumar L, Brenner N, Sledzieski S, Olaosebikan M, Roger LM, Lynn-Goin M, Klein-Seetharaman R, Berger B, Putnam H, Yang J, Lewinski NA, Singh R, Daniels NM, Cowen L, Klein-Seetharaman J. Transfer of knowledge from model organisms to evolutionarily distant non-model organisms: The coral Pocillopora damicornis membrane signaling receptome. Plos One. 18: e0270965. PMID 36735673 DOI: 10.1371/journal.pone.0270965  0.551
2022 Zaman S, Sledzieski S, Berger B, Wu YC, Bansal MS. virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 36125448 DOI: 10.1089/cmb.2021.0507  0.665
2022 Singh R, Devkota K, Sledzieski S, Berger B, Cowen L. Topsy-Turvy: integrating a global view into sequence-based PPI prediction. Bioinformatics (Oxford, England). 38: i264-i272. PMID 35758793 DOI: 10.1093/bioinformatics/btac258  0.589
2021 Sledzieski S, Singh R, Cowen L, Berger B. D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions. Cell Systems. PMID 34536380 DOI: 10.1016/j.cels.2021.08.010  0.574
2021 Ekim B, Berger B, Chikhi R. Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer. Cell Systems. PMID 34525345 DOI: 10.1016/j.cels.2021.08.009  0.777
2020 Berger E, Yorukoglu D, Zhang L, Nyquist SK, Shalek AK, Kellis M, Numanagić I, Berger B. Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets. Nature Communications. 11: 4662. PMID 32938926 DOI: 10.1038/S41467-020-18320-Z  0.569
2020 DeMeo B, Berger B. Hopper: a mathematically optimal algorithm for sketching biological data. Bioinformatics (Oxford, England). 36: i236-i241. PMID 32657375 DOI: 10.1093/Bioinformatics/Btaa408  0.338
2020 Cho H, Simmons S, Kim R, Berger B. Privacy-Preserving Biomedical Database Queries with Optimal Privacy-Utility Trade-Offs. Cell Systems. PMID 32359425 DOI: 10.1016/J.Cels.2020.03.006  0.317
2020 Berger B, Waterman MS, Yu YW. Levenshtein Distance, Sequence Comparison and Biological Database Search Ieee Transactions On Information Theory. 1-1. DOI: 10.1109/Tit.2020.2996543  0.337
2019 Berger B, Cho H. Emerging technologies towards enhancing privacy in genomic data sharing. Genome Biology. 20: 128. PMID 31262363 DOI: 10.1186/S13059-019-1741-0  0.336
2019 Hie B, Cho H, DeMeo B, Bryson B, Berger B. Geometric Sketching Compactly Summarizes the Single-Cell Transcriptomic Landscape. Cell Systems. PMID 31176620 DOI: 10.1016/J.Cels.2019.05.003  0.318
2019 Hie B, Bryson B, Berger B. Efficient integration of heterogeneous single-cell transcriptomes using Scanorama. Nature Biotechnology. PMID 31061482 DOI: 10.1038/S41587-019-0113-3  0.311
2018 Numanagic I, Gökkaya AS, Zhang L, Berger B, Alkan C, Hach F. Fast characterization of segmental duplications in genome assemblies. Bioinformatics (Oxford, England). 34: i706-i714. PMID 30423092 DOI: 10.1093/Bioinformatics/Bty586  0.388
2018 Shajii A, Numanagić I, Whelan C, Berger B. Statistical Binning for Barcoded Reads Improves Downstream Analyses. Cell Systems. 7: 219-226.e5. PMID 30138581 DOI: 10.1016/J.Cels.2018.07.005  0.401
2018 Luo Y, Yu YW, Zeng J, Berger B, Peng J. Metagenomic binning through low-density hashing. Bioinformatics (Oxford, England). PMID 30010790 DOI: 10.1093/Bioinformatics/Bty611  0.322
2018 Cho H, Wu DJ, Berger B. Secure genome-wide association analysis using multiparty computation. Nature Biotechnology. PMID 29734293 DOI: 10.1038/Nbt.4108  0.354
2018 Numanagić I, Malikić S, Ford M, Qin X, Toji L, Radovich M, Skaar TC, Pratt VM, Berger B, Scherer S, Sahinalp SC. Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes. Nature Communications. 9: 828. PMID 29483503 DOI: 10.1038/S41467-018-03273-1  0.37
2018 Orenstein Y, Ohler U, Berger B. Finding RNA structure in the unstructured RBPome. Bmc Genomics. 19: 154. PMID 29463232 DOI: 10.1186/S12864-018-4540-1  0.34
2017 Liu Y, Palmedo P, Ye Q, Berger B, Peng J. Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks. Cell Systems. PMID 29275173 DOI: 10.1016/J.Cels.2017.11.014  0.411
2017 Orenstein Y, Puccinelli R, Kim R, Fordyce P, Berger B. Optimized Sequence Library Design for Efficient In Vitro Interaction Mapping. Cell Systems. 5: 230-236.e5. PMID 28957657 DOI: 10.1016/J.Cels.2017.07.006  0.304
2017 Ma CY, Phoebe Chen YP, Berger B, Liao CS. Identification of Protein Complexes by Integrating Multiple Alignment of Protein Interaction Networks. Bioinformatics (Oxford, England). PMID 28130237 DOI: 10.1093/Bioinformatics/Btx043  0.335
2016 Cho H, Berger B, Peng J. Compact Integration of Multi-Network Topology for Functional Analysis of Genes. Cell Systems. PMID 27889536 DOI: 10.1016/J.Cels.2016.10.017  0.353
2016 Toth-Petroczy A, Palmedo P, Ingraham J, Hopf TA, Berger B, Sander C, Marks DS. Structured States of Disordered Proteins from Genomic Sequences. Cell. 167: 158-170.e12. PMID 27662088 DOI: 10.1016/J.Cell.2016.09.010  0.348
2016 Shajii A, Yorukoglu D, William Yu Y, Berger B. Fast genotyping of known SNPs through approximate k-mer matching. Bioinformatics (Oxford, England). 32: i538-i544. PMID 27587672 DOI: 10.1093/Bioinformatics/Btw460  0.326
2016 Simmons S, Sahinalp C, Berger B. Enabling Privacy-Preserving GWASs in Heterogeneous Human Populations. Cell Systems. 3: 54-61. PMID 27453444 DOI: 10.1016/J.Cels.2016.04.013  0.355
2016 Orenstein Y, Wang Y, Berger B. RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data. Bioinformatics (Oxford, England). 32: i351-i359. PMID 27307637 DOI: 10.1093/Bioinformatics/Btw259  0.366
2016 Cho H, Berger B, Peng J. Reconstructing Causal Biological Networks through Active Learning. Plos One. 11: e0150611. PMID 26930205 DOI: 10.1371/Journal.Pone.0150611  0.317
2016 Simmons S, Berger B. Realizing Privacy Preserving Genome-wide Association Studies. Bioinformatics (Oxford, England). PMID 26769317 DOI: 10.1093/Bioinformatics/Btw009  0.351
2015 Orenstein Y, Berger B. Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 26713687 DOI: 10.1089/Cmb.2015.0179  0.31
2015 Chirn GW, Rahman R, Sytnikova YA, Matts JA, Zeng M, Gerlach D, Yu M, Berger B, Naramura M, Kile BT, Lau NC. Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals. Plos Genetics. 11: e1005652. PMID 26588211 DOI: 10.1371/Journal.Pgen.1005652  0.361
2015 Yu YW, Daniels NM, Danko DC, Berger B. Entropy-scaling search of massive biological data. Cell Systems. 1: 130-140. PMID 26436140 DOI: 10.1016/J.Cels.2015.08.004  0.32
2015 Simmons S, Peng J, Bienkowska J, Berger B. Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 715-28. PMID 26098139 DOI: 10.1089/Cmb.2015.0085  0.328
2015 Karp PD, Berger B, Kovats D, Lengauer T, Linial M, Sabeti P, Hide W, Rost B. ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus. F1000research. 4: 12. PMID 26097686 DOI: 10.1371/Journal.Pcbi.1004087  0.349
2015 Wang S, Cho H, Zhai C, Berger B, Peng J. Exploiting ontology graph for predicting sparsely annotated gene function. Bioinformatics (Oxford, England). 31: i357-i364. PMID 26072504 DOI: 10.1093/Bioinformatics/Btv260  0.375
2015 Karp PD, Berger B, Kovats D, Lengauer T, Linial M, Sabeti P, Hide W, Rost B. Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus. Bioinformatics (Oxford, England). 31: 616-7. PMID 25644272 DOI: 10.1093/Bioinformatics/Btv019  0.35
2014 Chindelevitch L, Trigg J, Regev A, Berger B. An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models. Nature Communications. 5: 4893. PMID 25291352 DOI: 10.1038/Ncomms5893  0.303
2014 Taipale M, Tucker G, Peng J, Krykbaeva I, Lin ZY, Larsen B, Choi H, Berger B, Gingras AC, Lindquist S. A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways. Cell. 158: 434-48. PMID 25036637 DOI: 10.1016/J.Cell.2014.05.039  0.345
2014 Waldispühl J, O'Donnell CW, Will S, Devadas S, Backofen R, Berger B. Simultaneous alignment and folding of protein sequences Journal of Computational Biology. 21: 477-491. PMID 24766258 DOI: 10.1089/Cmb.2013.0163  0.41
2014 Berger E, Yorukoglu D, Peng J, Berger B. HapTree: a novel Bayesian framework for single individual polyplotyping using NGS data. Plos Computational Biology. 10: e1003502. PMID 24675685 DOI: 10.1371/Journal.Pcbi.1003502  0.408
2014 Meyer P, Cokelaer T, Chandran D, Kim KH, Loh PR, Tucker G, Lipson M, Berger B, Kreutz C, Raue A, Steiert B, Timmer J, Bilal E, Dream Six and Seven Parameter Estimation Consortium, Sauro HM, et al. Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. Bmc Systems Biology. 8: 13. PMID 24507381 DOI: 10.1186/1752-0509-8-13  0.316
2013 Tucker G, Loh PR, Berger B. A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis Bmc Bioinformatics. 14. PMID 24093595 DOI: 10.1186/1471-2105-14-299  0.324
2013 Chindelevitch L, Ma CY, Liao CS, Berger B. Optimizing a global alignment of protein interaction networks. Bioinformatics (Oxford, England). 29: 2765-73. PMID 24048352 DOI: 10.1093/Bioinformatics/Btt486  0.336
2013 Daniels NM, Gallant A, Peng J, Cowen LJ, Baym M, Berger B. Compressive genomics for protein databases. Bioinformatics (Oxford, England). 29: i283-90. PMID 23812995 DOI: 10.1093/Bioinformatics/Btt214  0.773
2013 Lipson M, Loh PR, Levin A, Reich D, Patterson N, Berger B. Efficient moment-based inference of admixture parameters and sources of gene flow. Molecular Biology and Evolution. 30: 1788-802. PMID 23709261 DOI: 10.1093/Molbev/Mst099  0.308
2013 Berger B, Peng J, Singh M. Computational solutions for omics data. Nature Reviews. Genetics. 14: 333-46. PMID 23594911 DOI: 10.1038/Nrg3433  0.569
2013 Ma CY, Lin SH, Lee CC, Tang CY, Berger B, Liao CS. Reconstruction of phyletic trees by global alignment of multiple metabolic networks. Bmc Bioinformatics. 14: S12. PMID 23368411 DOI: 10.1186/1471-2105-14-S2-S12  0.31
2013 Will S, Yu M, Berger B. Structure-based whole-genome realignment reveals many novel noncoding RNAs. Genome Research. 23: 1018-27. PMID 23296921 DOI: 10.1101/Gr.137091.111  0.404
2012 Washietl S, Will S, Hendrix DA, Goff LA, Rinn JL, Berger B, Kellis M. Computational analysis of noncoding RNAs. Wiley Interdisciplinary Reviews. Rna. 3: 759-78. PMID 22991327 DOI: 10.1002/Wrna.1134  0.757
2012 Hosur R, Peng J, Vinayagam A, Stelzl U, Xu J, Perrimon N, Bienkowska J, Berger B. A computational framework for boosting confidence in high-throughput protein-protein interaction datasets. Genome Biology. 13: R76. PMID 22937800 DOI: 10.1186/Gb-2012-13-8-R76  0.372
2012 Loh PR, Baym M, Berger B. Compressive genomics. Nature Biotechnology. 30: 627-30. PMID 22781691 DOI: 10.1038/nbt.2241  0.674
2012 Daniels NM, Hosur R, Berger B, Cowen LJ. SMURFLite: Combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone Bioinformatics. 28: 1216-1222. PMID 22408192 DOI: 10.1093/Bioinformatics/Bts110  0.579
2012 Bryan AW, O'Donnell CW, Menke M, Cowen LJ, Lindquist S, Berger B. STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions. Proteins. 80: 410-20. PMID 22095906 DOI: 10.1002/Prot.23203  0.569
2012 Gong P, Loh PR, Barker ND, Tucker G, Wang N, Zhang C, Escalon BL, Berger B, Perkins EJ. Building quantitative prediction models for tissue residue of two explosives compounds in earthworms from microarray gene expression data. Environmental Science & Technology. 46: 19-26. PMID 21776976 DOI: 10.1021/Es201187U  0.337
2011 Loh PR, Tucker G, Berger B. Phenotype prediction using regularized regression on genetic data in the DREAM5 Systems Genetics B Challenge. Plos One. 6: e29095. PMID 22216175 DOI: 10.1371/Journal.Pone.0029095  0.334
2011 Adams DJ, Berger B, Harismendy O, Huttenhower C, Liu XS, Myers CL, Oshlack A, Rinn JL, Walhout AJ. Genomics in 2011: challenges and opportunities. Genome Biology. 12: 137. PMID 22204305 DOI: 10.1186/Gb-2011-12-12-137  0.316
2011 Friedman AA, Tucker G, Singh R, Yan D, Vinayagam A, Hu Y, Binari R, Hong P, Sun X, Porto M, Pacifico S, Murali T, Finley RL, Asara JM, Berger B, et al. Proteomic and functional genomic landscape of receptor tyrosine kinase and ras to extracellular signal-regulated kinase signaling. Science Signaling. 4: rs10. PMID 22028469 DOI: 10.1126/Scisignal.2002029  0.32
2011 Shenker S, O'Donnell CW, Devadas S, Berger B, Waldispühl J. Efficient traversal of beta-sheet protein folding pathways using ensemble models. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 1635-47. PMID 21958108 DOI: 10.1089/Cmb.2011.0176  0.35
2011 Trigg J, Gutwin K, Keating AE, Berger B. Multicoil2: Predicting coiled coils and their oligomerization states from sequence in the twilight zone Plos One. 6. PMID 21901122 DOI: 10.1371/Journal.Pone.0023519  0.392
2011 Hu Y, Flockhart I, Vinayagam A, Bergwitz C, Berger B, Perrimon N, Mohr SE. An integrative approach to ortholog prediction for disease-focused and other functional studies. Bmc Bioinformatics. 12: 357. PMID 21880147 DOI: 10.1186/1471-2105-12-357  0.384
2011 Park D, Singh R, Baym M, Liao CS, Berger B. IsoBase: a database of functionally related proteins across PPI networks. Nucleic Acids Research. 39: D295-300. PMID 21177658 DOI: 10.1093/Nar/Gkq1234  0.73
2011 Hosur R, Xu J, Bienkowska J, Berger B. iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions. Journal of Molecular Biology. 405: 1295-310. PMID 21130772 DOI: 10.1016/J.Jmb.2010.11.025  0.324
2010 Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, ... ... Berger B, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.). 330: 1787-97. PMID 21177974 DOI: 10.1126/Science.1198374  0.704
2010 Singh R, Park D, Xu J, Hosur R, Berger B. Struct2Net: a web service to predict protein-protein interactions using a structure-based approach. Nucleic Acids Research. 38: W508-15. PMID 20513650 DOI: 10.1093/Nar/Gkq481  0.395
2010 Menke M, Berger B, Cowen L. Markov random fields reveal an N-terminal double beta-propeller motif as part of a bacterial hybrid two-component sensor system. Proceedings of the National Academy of Sciences of the United States of America. 107: 4069-74. PMID 20147619 DOI: 10.1073/Pnas.0909950107  0.605
2010 Nir O, Bakal C, Perrimon N, Berger B. Inference of RhoGAP/GTPase regulation using single-cell morphological data from a combinatorial RNAi screen. Genome Research. 20: 372-80. PMID 20144944 DOI: 10.1101/Gr.100248.109  0.358
2009 Lun DS, Rockwell G, Guido NJ, Baym M, Kelner JA, Berger B, Galagan JE, Church GM. Large-scale identification of genetic design strategies using local search. Molecular Systems Biology. 5: 296. PMID 19690565 DOI: 10.1038/Msb.2009.57  0.684
2009 Kaplow IM, Singh R, Friedman A, Bakal C, Perrimon N, Berger B. RNAiCut: automated detection of significant genes from functional genomic screens. Nature Methods. 6: 476-7. PMID 19564846 DOI: 10.1038/Nmeth0709-476  0.319
2009 Waldispühl J, Devadas S, Berger B, Clote P. RNAmutants: a web server to explore the mutational landscape of RNA secondary structures. Nucleic Acids Research. 37: W281-6. PMID 19531740 DOI: 10.1093/Nar/Gkp477  0.355
2009 Liao CS, Lu K, Baym M, Singh R, Berger B. IsoRankN: spectral methods for global alignment of multiple protein networks. Bioinformatics (Oxford, England). 25: i253-8. PMID 19477996 DOI: 10.1093/Bioinformatics/Btp203  0.694
2009 Bryan AW, Menke M, Cowen LJ, Lindquist SL, Berger B. BETASCAN: probable beta-amyloids identified by pairwise probabilistic analysis. Plos Computational Biology. 5: e1000333. PMID 19325876 DOI: 10.1371/Journal.Pcbi.1000333  0.557
2008 Singh R, Xu J, Berger B. Global alignment of multiple protein interaction networks with application to functional orthology detection. Proceedings of the National Academy of Sciences of the United States of America. 105: 12763-8. PMID 18725631 DOI: 10.1073/Pnas.0806627105  0.366
2008 Pulim V, Berger B, Bienkowska J. Optimal contact map alignment of protein-protein interfaces. Bioinformatics (Oxford, England). 24: 2324-8. PMID 18710876 DOI: 10.1093/Bioinformatics/Btn432  0.385
2008 Waldispühl J, Devadas S, Berger B, Clote P. Efficient algorithms for probing the RNA mutation landscape. Plos Computational Biology. 4: e1000124. PMID 18688270 DOI: 10.1371/Journal.Pcbi.1000124  0.354
2008 Menke M, Berger B, Cowen L. Matt: local flexibility aids protein multiple structure alignment. Plos Computational Biology. 4: e10. PMID 18193941 DOI: 10.1371/Journal.Pcbi.0040010  0.602
2008 Pulim V, Bienkowska J, Berger B. LTHREADER: prediction of extracellular ligand-receptor interactions in cytokines using localized threading. Protein Science : a Publication of the Protein Society. 17: 279-92. PMID 18096641 DOI: 10.1110/Ps.073178108  0.354
2008 Waldispühl J, O'Donnell CW, Devadas S, Clote P, Berger B. Modeling ensembles of transmembrane beta-barrel proteins. Proteins. 71: 1097-112. PMID 18004792 DOI: 10.1002/Prot.21788  0.34
2007 Sterner B, Singh R, Berger B. Predicting and annotating catalytic residues: an information theoretic approach. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 14: 1058-73. PMID 17887954 DOI: 10.1089/Cmb.2007.0042  0.369
2007 Xu J, Jiao F, Berger B. A parameterized algorithm for protein structure alignment. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 14: 564-77. PMID 17683261 DOI: 10.1089/Cmb.2007.R003  0.33
2006 Waldispühl J, Berger B, Clote P, Steyaert JM. Predicting transmembrane beta-barrels and interstrand residue interactions from sequence. Proteins. 65: 61-74. PMID 16858668 DOI: 10.1002/Prot.21046  0.41
2006 Waldispühl J, Berger B, Clote P, Steyaert J. transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels Nucleic Acids Research. 34: 189-193. PMID 16844989 DOI: 10.1093/Nar/Gkl205  0.336
2006 Junker M, Schuster CC, McDonnell AV, Sorg KA, Finn MC, Berger B, Clark PL. Pertactin beta-helix folding mechanism suggests common themes for the secretion and folding of autotransporter proteins. Proceedings of the National Academy of Sciences of the United States of America. 103: 4918-23. PMID 16549796 DOI: 10.1073/Pnas.0507923103  0.31
2006 McDonnell AV, Menke M, Palmer N, King J, Cowen L, Berger B. Fold recognition and accurate sequence-structure alignment of sequences directing beta-sheet proteins. Proteins. 63: 976-85. PMID 16547930 DOI: 10.1002/Prot.20942  0.578
2006 Uetz P, Dong YA, Zeretzke C, Atzler C, Baiker A, Berger B, Rajagopala SV, Roupelieva M, Rose D, Fossum E, Haas J. Herpesviral protein networks and their interaction with the human proteome. Science (New York, N.Y.). 311: 239-42. PMID 16339411 DOI: 10.1126/Science.1116804  0.315
2006 McDonnell AV, Jiang T, Keating AE, Berger B. Paircoil2: Improved prediction of coiled coils from sequence Bioinformatics. 22: 356-358. PMID 16317077 DOI: 10.1093/Bioinformatics/Bti797  0.381
2006 Xu J, Berger B. Fast and accurate algorithms for protein side-chain packing Journal of the Acm (Jacm). 53: 533-557. DOI: 10.1145/1162349.1162350  0.344
2005 Menke M, King J, Berger B, Cowen L. Wrap-and-Pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 12: 777-95. PMID 16108716 DOI: 10.1089/Cmb.2005.12.777  0.55
2005 Schwartz R, Shor PW, Berger B. Local rule simulations of capsid assembly Journal of Theoretical Medicine. 6: 81-85. DOI: 10.1080/10273660500149257  0.487
2004 Coventry A, Kleitman DJ, Berger B. MSARI: multiple sequence alignments for statistical detection of RNA secondary structure. Proceedings of the National Academy of Sciences of the United States of America. 101: 12102-7. PMID 15304649 DOI: 10.1073/Pnas.0404193101  0.628
2004 Kellis M, Patterson N, Birren B, Berger B, Lander ES. Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 319-55. PMID 15285895 DOI: 10.1089/1066527041410319  0.672
2002 Bradley P, Kim PS, Berger B. TRILOGY: Discovery of sequence-structure patterns across diverse proteins. Proceedings of the National Academy of Sciences of the United States of America. 99: 8500-5. PMID 12084910 DOI: 10.1073/Pnas.112221999  0.366
2002 Cowen L, Bradley P, Menke M, King J, Berger B. Predicting the beta-helix fold from protein sequence data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 9: 261-76. PMID 12015881 DOI: 10.1089/10665270252935458  0.565
2002 Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. ARACHNE: a whole-genome shotgun assembler. Genome Research. 12: 177-89. PMID 11779843 DOI: 10.1101/gr.208902  0.453
2001 Bradley P, Cowen L, Menke M, King J, Berger B. BETAWRAP: successful prediction of parallel beta -helices from primary sequence reveals an association with many microbial pathogens. Proceedings of the National Academy of Sciences of the United States of America. 98: 14819-24. PMID 11752429 DOI: 10.1073/Pnas.251267298  0.579
2000 Batzoglou S, Pachter L, Mesirov JP, Berger B, Lander ES. Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Research. 10: 950-8. PMID 10899144 DOI: 10.1101/Gr.10.7.950  0.653
2000 Schwartz R, Garcea RL, Berger B. "Local rules" theory applied to polyomavirus polymorphic capsid assemblies. Virology. 268: 461-70. PMID 10704354 DOI: 10.1006/Viro.1999.0180  0.507
2000 Berger B, King J, Schwartz R, Shor P. Local rule mechanism for selecting icosahedral shell geometry Discrete Applied Mathematics. 104: 97-111. DOI: 10.1016/S0166-218X(00)00187-6  0.487
1999 Batzoglou S, Berger B, Mesirov J, Lander ES. Sequencing a genome by walking with clone-end sequences: a mathematical analysis. Genome Research. 9: 1163-74. PMID 10613838 DOI: 10.1101/Gr.9.12.1163  0.529
1999 Pachter L, Batzoglou S, Spitkovsky VI, Banks E, Lander ES, Kleitman DJ, Berger B. A dictionary-based approach for gene annotation. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 6: 419-30. PMID 10582576 DOI: 10.1089/106652799318364  0.786
1999 Singh M, Berger B, Kim PS. LearnCoil-VMF: Computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins Journal of Molecular Biology. 290: 1031-1041. PMID 10438601 DOI: 10.1006/Jmbi.1999.2796  0.549
1998 Schwartz R, Shor PW, Prevelige PE, Berger B. Local rules simulation of the kinetics of virus capsid self-assembly Biophysical Journal. 75: 2626-2636. PMID 9826587 DOI: 10.1016/S0006-3495(98)77708-2  0.494
1998 Singh M, Berger B, Kim PS, Berger JM, Cochran AG. Computational learning reveals coiled coil-like motifs in histidine kinase linker domains. Proceedings of the National Academy of Sciences of the United States of America. 95: 2738-43. PMID 9501159 DOI: 10.1073/Pnas.95.6.2738  0.552
1998 Awerbuch B, Berger B, Cowen L, Peleg D. Near-Linear Time Construction of Sparse Neighborhood Covers Siam Journal On Computing. 28: 263-277. DOI: 10.1137/S0097539794271898  0.519
1997 Berger B, Singh M. An iterative method for improved protein structural motif recognition. Journal of Computational Biology. 4: 261-273. PMID 9278059 DOI: 10.1089/Cmb.1997.4.261  0.56
1997 Wolf E, Kim PS, Berger B. MultiCoil: A program for predicting two- and three-stranded coiled coils Protein Science. 6: 1179-1189. PMID 9194178 DOI: 10.1002/Pro.5560060606  0.308
1996 Awerbuch B, Berger B, Cowen L, Peleg D. Fast distributed network decompositions and covers Journal of Parallel and Distributed Computing. 39: 105-114. DOI: 10.1006/Jpdc.1996.0159  0.529
1995 Berger B, Wilson DB, Wolf E, Tonchev T, Milla M, Kim PS. Predicting coiled coils by use of pairwise residue correlations Proceedings of the National Academy of Sciences of the United States of America. 92: 8259-8263. PMID 7667278 DOI: 10.1073/Pnas.92.18.8259  0.31
1995 Berger B. Algorithms for protein structural motif recognition. Journal of Computational Biology. 2: 125-138. PMID 7497115 DOI: 10.1089/Cmb.1995.2.125  0.376
1995 Berger B, Cowen L. Scheduling with Concurrency-Based Constraints Journal of Algorithms. 18: 98-123. DOI: 10.1006/Jagm.1995.1003  0.518
1994 Berger B, Shor PW, Tucker-Kellogg L, King J. Local rule-based theory of virus shell assembly Proceedings of the National Academy of Sciences of the United States of America. 91: 7732-7736. PMID 8052652 DOI: 10.1073/Pnas.91.16.7732  0.645
1994 Awerbuch B, Berger B, Cowen L, Peleg D. Low-diameter graph decomposition is in NC Random Structures and Algorithms. 5: 441-452. DOI: 10.1002/Rsa.3240050305  0.507
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