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 |
0.555 |
|
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 |
0.528 |
|
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 |
0.552 |
|
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 |
0.59 |
|
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 |
0.575 |
|
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 |
0.572 |
|
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 |
0.402 |
|
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 |
0.323 |
|
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 |
0.349 |
|
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 |
0.57 |
|
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 |
0.675 |
|
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 |
0.58 |
|
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 |
0.57 |
|
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 |
0.606 |
|
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 |
0.32 |
|
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 |
0.356 |
|
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 |
0.603 |
|
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 |
0.551 |
|
2005 |
Schwartz R, Shor PW, Berger B. Local rule simulations of capsid assembly Journal of Theoretical Medicine. 6: 81-85. DOI: 10.1080/10273660500149257 |
0.488 |
|
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 |
0.674 |
|
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 |
0.566 |
|
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 |
0.454 |
|
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 |
0.58 |
|
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 |
0.656 |
|
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 |
0.53 |
|
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 |
0.787 |
|
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 |
0.55 |
|
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 |
0.553 |
|
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 |
0.52 |
|
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 |
0.561 |
|
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 |
0.53 |
|
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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