☰

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
Tree Info Similar researchers PubMed Report error

115/278 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  0.753
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  0.769
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  0.773
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  0.568
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  0.336
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  0.353
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  0.369
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  0.303
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  0.325
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  0.407
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  0.772
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  0.672
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
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 F1000research. 3. DOI: 10.7490/F1000Research.1090278.1  0.3
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  0.728
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  0.682
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  0.692
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  0.341
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  0.316
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  0.487
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  0.506
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  0.486
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  0.785
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  0.493
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  0.517
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  0.506
Low-probability matches (unlikely to be authored by this person)
2012 Schmid PR, Palmer NP, Kohane IS, Berger B. Making sense out of massive data by going beyond differential expression. Proceedings of the National Academy of Sciences of the United States of America. 109: 5594-9. PMID 22447773 DOI: 10.1073/Pnas.1118792109  0.3
2011 Halfmann R, Alberti S, Krishnan R, Lyle N, O'Donnell CW, King OD, Berger B, Pappu RV, Lindquist S. Opposing effects of glutamine and asparagine govern prion formation by intrinsically disordered proteins. Molecular Cell. 43: 72-84. PMID 21726811 DOI: 10.1016/J.Molcel.2011.05.013  0.299
2011 Bryan AW, Starner-Kreinbrink JL, Hosur R, Clark PL, Berger B. Structure-based prediction reveals capping motifs that inhibit β-helix aggregation. Proceedings of the National Academy of Sciences of the United States of America. 108: 11099-104. PMID 21685332 DOI: 10.1073/Pnas.1017504108  0.297
2022 Berger B, Yu YW. Navigating bottlenecks and trade-offs in genomic data analysis. Nature Reviews. Genetics. PMID 36476810 DOI: 10.1038/s41576-022-00551-z  0.297
2014 Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K, Sudmant PH, Schraiber JG, Castellano S, Lipson M, Berger B, Economou C, Bollongino R, Fu Q, Bos KI, et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature. 513: 409-13. PMID 25230663 DOI: 10.1038/Nature13673  0.296
2015 Tucker G, Loh PR, MacLeod IM, Hayes BJ, Goddard ME, Berger B, Price AL. Two-Variance-Component Model Improves Genetic Prediction in Family Datasets. American Journal of Human Genetics. 97: 677-90. PMID 26544803 DOI: 10.1016/J.Ajhg.2015.10.002  0.295
2011 Hosur R, Singh R, Berger B. Sparse estimation for structural variability. Algorithms For Molecular Biology : Amb. 6: 12. PMID 21504605 DOI: 10.1186/1748-7188-6-12  0.295
2020 Nazeen S, Yu YW, Berger B. Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads. Genome Biology. 21: 47. PMID 32093762 DOI: 10.1186/S13059-020-1933-7  0.295
2016 Berger B, Gaasterland T, Lengauer T, Orengo C, Gaeta B, Markel S, Valencia A. ISCB's Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing. Plos Computational Biology. 12: e1004816. PMID 27010398 DOI: 10.1371/Journal.Pcbi.1004816  0.294
2019 Hutchison L, Berger B, Kohane I. Meta-analysis of C. elegans single-cell developmental data reveals multi-frequency oscillation in gene activation. Bioinformatics (Oxford, England). PMID 31860066 DOI: 10.1093/Bioinformatics/Btz864  0.294
2013 Loh PR, Lipson M, Patterson N, Moorjani P, Pickrell JK, Reich D, Berger B. Inferring admixture histories of human populations using linkage disequilibrium. Genetics. 193: 1233-54. PMID 23410830 DOI: 10.1534/Genetics.112.147330  0.294
1998 Hobbs LW, Jesurum CE, Pulim V, Berger B. Local topology of silica networks Philosophical Magazine. 78: 679-711. DOI: 10.1080/01418619808241930  0.292
2016 Yorukoglu D, Yu YW, Peng J, Berger B. Compressive mapping for next-generation sequencing. Nature Biotechnology. 34: 374-376. PMID 27054987 DOI: 10.1038/Nbt.3511  0.289
1999 Berger B, Hoest GW, Paulson JR, Shor PW. On the structure of the scaffolding core of bacteriophage T4. Journal of Computational Biology. 6: 1-12. PMID 10223661 DOI: 10.1089/Cmb.1999.6.1  0.289
1998 Berger B, Leighton T. Protein folding in the hydrophobic-hydrophilic (HP) model is NP-complete. Journal of Computational Biology. 5: 27-40. PMID 9541869 DOI: 10.1089/Cmb.1998.5.27  0.289
2016 Berger B, Daniels NM, Yu YW. Algorithmic advances take advantage of the structure of massive biological data landscape: Computational Biology in the 21(st) Century: Scaling with Compressive Algorithms. Communications of the Acm. 59: 72-80. PMID 28966343 DOI: 10.1145/2957324  0.289
2015 Sahni N, Yi S, Taipale M, Fuxman Bass JI, Coulombe-Huntington J, Yang F, Peng J, Weile J, Karras GI, Wang Y, Kovács IA, Kamburov A, Krykbaeva I, Lam MH, Tucker G, ... ... Berger B, et al. Widespread macromolecular interaction perturbations in human genetic disorders. Cell. 161: 647-60. PMID 25910212 DOI: 10.1016/J.Cell.2015.04.013  0.286
2012 Chindelevitch L, Stanley S, Hung D, Regev A, Berger B. MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis. Genome Biology. 13: r6. PMID 22292986 DOI: 10.1186/Gb-2012-13-1-R6  0.286
2013 Moorjani P, Patterson N, Loh PR, Lipson M, Kisfali P, Melegh BI, Bonin M, Kádaši L, Rieß O, Berger B, Reich D, Melegh B. Reconstructing Roma history from genome-wide data. Plos One. 8: e58633. PMID 23516520 DOI: 10.1371/Journal.Pone.0058633  0.285
2009 Tian Z, Palmer N, Schmid P, Yao H, Galdzicki M, Berger B, Wu E, Kohane IS. A practical platform for blood biomarker study by using global gene expression profiling of peripheral whole blood. Plos One. 4: e5157. PMID 19381341 DOI: 10.1371/Journal.Pone.0005157  0.285
2012 Chindelevitch L, Loh PR, Enayetallah A, Berger B, Ziemek D. Assessing statistical significance in causal graphs. Bmc Bioinformatics. 13: 35. PMID 22348444 DOI: 10.1186/1471-2105-13-35  0.283
2021 Berger B, Waterman MS, Yu YW. Levenshtein Distance, Sequence Comparison and Biological Database Search. Ieee Transactions On Information Theory. 67: 3287-3294. PMID 34257466 DOI: 10.1109/tit.2020.2996543  0.283
2011 Schnall-Levin M, Rissland OS, Johnston WK, Perrimon N, Bartel DP, Berger B. Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs. Genome Research. 21: 1395-403. PMID 21685129 DOI: 10.1101/Gr.121210.111  0.282
2015 Loh PR, Tucker G, Bulik-Sullivan BK, Vilhjálmsson BJ, Finucane HK, Salem RM, Chasman DI, Ridker PM, Neale BM, Berger B, Patterson N, Price AL. Efficient Bayesian mixed-model analysis increases association power in large cohorts. Nature Genetics. 47: 284-90. PMID 25642633 DOI: 10.1038/Ng.3190  0.281
2018 Orenstein Y, Yu YW, Berger B. Joker de Bruijn: Covering k-Mers Using Joker Characters. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 30117747 DOI: 10.1089/Cmb.2018.0032  0.281
2015 Chindelevitch L, Trigg J, Regev A, Berger B. Reply to "Do genome-scale models need exact solvers or clearer standards?". Molecular Systems Biology. 11: 830. PMID 26467283 DOI: 10.15252/Msb.20156548  0.281
2020 Kazer SW, Aicher TP, Muema DM, Carroll SL, Ordovas-Montanes J, Miao VN, Tu AA, Ziegler CGK, Nyquist SK, Wong EB, Ismail N, Dong M, Moodley A, Berger B, Love JC, et al. Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection. Nature Medicine. PMID 32251406 DOI: 10.1038/S41591-020-0799-2  0.279
2015 Lipson M, Loh PR, Sankararaman S, Patterson N, Berger B, Reich D. Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes. Plos Genetics. 11: e1005550. PMID 26562831 DOI: 10.1371/Journal.Pgen.1005550  0.278
1996 Jesurum CE, Pulimt V, Berger B, Hobbst LW. Modeling Amorphization of Tetrahedral Structures Using Local Approaches Mrs Proceedings. 439. DOI: 10.1557/Proc-439-633  0.278
2018 Cho H, Berger B, Peng J. Generalizable and Scalable Visualization of Single-Cell Data Using Neural Networks. Cell Systems. PMID 29936184 DOI: 10.1016/J.Cels.2018.05.017  0.276
2012 Pickrell JK, Patterson N, Barbieri C, Berthold F, Gerlach L, Güldemann T, Kure B, Mpoloka SW, Nakagawa H, Naumann C, Lipson M, Loh PR, Lachance J, Mountain J, Bustamante CD, ... Berger B, et al. The genetic prehistory of southern Africa. Nature Communications. 3: 1143. PMID 23072811 DOI: 10.1038/Ncomms2140  0.276
2020 Ziegler CGK, Allon SJ, Nyquist SK, Mbano IM, Miao VN, Tzouanas CN, Cao Y, Yousif AS, Bals J, Hauser BM, Feldman J, Muus C, Wadsworth MH, Kazer SW, Hughes TK, ... ... Berger B, et al. SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues. Cell. PMID 32413319 DOI: 10.1016/J.Cell.2020.04.035  0.275
1998 Berger B, Shor PW. On the Structure of the Scaffolding Core of Bacteriophage T4 and Its Role in Head Length Determination Journal of Structural Biology. 121: 285-294. PMID 9705877 DOI: 10.1006/Jsbi.1997.3942  0.273
2017 Fogg CN, Kovats DE, Berger B. 2017 ISCB Accomplishment by a Senior Scientist Award: Pavel Pevzner. F1000research. 6. PMID 28713548 DOI: 10.12688/F1000Research.11588.1  0.27
2008 Wieland SC, Cassa CA, Mandl KD, Berger B. Revealing the spatial distribution of a disease while preserving privacy. Proceedings of the National Academy of Sciences of the United States of America. 105: 17608-13. PMID 19015533 DOI: 10.1073/Pnas.0801021105  0.269
2017 Fogg CN, Kovats D, Berger B. 2017 ISCB Innovator Award: Aviv Regev. F1000research. 6. PMID 28713547 DOI: 10.12688/F1000Research.11585.1  0.268
2012 Garcia-Reyero N, Escalon BL, Loh PR, Laird JG, Kennedy AJ, Berger B, Perkins EJ. Assessment of chemical mixtures and groundwater effects on Daphnia magna transcriptomics. Environmental Science & Technology. 46: 42-50. PMID 21744839 DOI: 10.1021/Es201245B  0.267
2006 Singh R, Xu J, Berger B. Struct2net: integrating structure into protein-protein interaction prediction. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 403-14. PMID 17094256  0.266
2017 Fogg CN, Kovats DE, Berger B. 2017 ISCB Overton Prize: Christoph Bock. F1000research. 6. PMID 28713546 DOI: 10.12688/F1000Research.11586.1  0.264
1997 Berger B. The Fourth Moment Method Siam Journal On Computing. 26: 1188-1207. DOI: 10.1137/S0097539792240005  0.263
2019 Bepler T, Morin A, Rapp M, Brasch J, Shapiro L, Noble AJ, Berger B. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nature Methods. PMID 31591578 DOI: 10.1038/S41592-019-0575-8  0.259
1999 Berger B, Kleinberg J, Leighton T. Reconstructing a three-dimensional model with arbitrary errors Journal of the Acm (Jacm). 46: 212-235. DOI: 10.1145/301970.301972  0.259
2010 Schnall-Levin M, Zhao Y, Perrimon N, Berger B. Conserved microRNA targeting in Drosophila is as widespread in coding regions as in 3'UTRs. Proceedings of the National Academy of Sciences of the United States of America. 107: 15751-6. PMID 20729470 DOI: 10.1073/Pnas.1006172107  0.258
2013 Bergwitz C, Wee MJ, Sinha S, Huang J, DeRobertis C, Mensah LB, Cohen J, Friedman A, Kulkarni M, Hu Y, Vinayagam A, Schnall-Levin M, Berger B, Perkins LA, Mohr SE, et al. Genetic determinants of phosphate response in Drosophila. Plos One. 8: e56753. PMID 23520455 DOI: 10.1371/Journal.Pone.0056753  0.257
1997 Jesurum CE, Pulim V, Hobbs LW, Berger B. Modeling of Topologically-Disordered Tetrahedral Network Structures using Local Rules Materials Science Forum. 37-40. DOI: 10.4028/Www.Scientific.Net/Msf.239-241.37  0.255
1998 Hobbs LW, Jesurum CE, Pulim V, Berger B. Topological modeling of cascade amorphization in network structures using local rules Materials Science and Engineering a-Structural Materials Properties Microstructure and Processing. 253: 16-29. DOI: 10.1016/S0921-5093(98)00706-0  0.254
1991 Berger B, Rompel J. Simulating (log c n )-wise independence in NC Journal of the Acm. 38: 1026-1046. DOI: 10.1145/115234.115347  0.252
2017 Fogg CN, Kovats DE, Berger B. 2017 Outstanding Contributions to ISCB Award: Fran Lewitter. F1000research. 6. PMID 28713545 DOI: 10.12688/F1000Research.11587.1  0.252
2007 Wieland SC, Brownstein JS, Berger B, Mandl KD. Automated real time constant-specificity surveillance for disease outbreaks. Bmc Medical Informatics and Decision Making. 7: 15. PMID 17567912 DOI: 10.1186/1472-6947-7-15  0.251
2020 Hie B, Peters J, Nyquist SK, Shalek AK, Berger B, Bryson BD. Computational Methods for Single-Cell RNA Sequencing Annual Review of Biomedical Data Science. 3. DOI: 10.1146/annurev-biodatasci-012220-100601  0.247
2013 Moorjani P, Thangaraj K, Patterson N, Lipson M, Loh PR, Govindaraj P, Berger B, Reich D, Singh L. Genetic evidence for recent population mixture in India. American Journal of Human Genetics. 93: 422-38. PMID 23932107 DOI: 10.1016/J.Ajhg.2013.07.006  0.247
2008 Wu E, Palmer N, Tian Z, Moseman AP, Galdzicki M, Wang X, Berger B, Zhang H, Kohane IS. Comprehensive dissection of PDGF-PDGFR signaling pathways in PDGFR genetically defined cells. Plos One. 3: e3794. PMID 19030102 DOI: 10.1371/Journal.Pone.0003794  0.246
2019 Brasch J, Goodman KM, Noble AJ, Rapp M, Mannepalli S, Bahna F, Dandey VP, Bepler T, Berger B, Maniatis T, Potter CS, Carragher B, Honig B, Shapiro L. Visualization of clustered protocadherin neuronal self-recognition complexes. Nature. PMID 30971825 DOI: 10.1038/s41586-019-1089-3  0.244
2021 Bepler T, Berger B. Learning the protein language: Evolution, structure, and function. Cell Systems. 12: 654-669.e3. PMID 34139171 DOI: 10.1016/j.cels.2021.05.017  0.243
2014 Lipson M, Loh PR, Patterson N, Moorjani P, Ko YC, Stoneking M, Berger B, Reich D. Reconstructing Austronesian population history in Island Southeast Asia. Nature Communications. 5: 4689. PMID 25137359 DOI: 10.1038/Ncomms5689  0.243
2011 Berger B. Preface: 14th International Conference on Research in Computational Molecular Biology (RECOMB 2010). Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 205. PMID 21385028 DOI: 10.1089/Cmb.2010.006P  0.24
1997 Berger B, Shor PW. Tight Bounds for the Maximum Acyclic Subgraph Problem Journal of Algorithms. 25: 1-18. DOI: 10.1006/Jagm.1997.0864  0.239
2008 Singh R, Xu J, Berger B. Global alignment of multiple protein interaction networks. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 303-14. PMID 18229695  0.238
2016 Valencia A, Markel S, Gaeta B, Gaasterland T, Lengauer T, Berger B, Orengo C. ISCB's initial reaction to New England Journal of Medicine editorial on data sharing. F1000research. 5. PMID 26998241 DOI: 10.12688/F1000Research.8051.1  0.237
2016 Alberti C, Daniels N, Hernaez M, Voges J, Goldfeder RL, Hernandez-Lopez AA, Mattavelli M, Berger B. An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values. Proceedings. Data Compression Conference. 2016: 221-230. PMID 28845445 DOI: 10.1109/DCC.2016.39  0.236
2023 Mendelsohn S, Froelicher D, Loginov D, Bernick D, Berger B, Cho H. sfkit: a web-based toolkit for secure and federated genomic analysis. Nucleic Acids Research. 51: W535-W541. PMID 37246709 DOI: 10.1093/nar/gkad464  0.235
2018 Ordovas-Montanes J, Dwyer DF, Nyquist SK, Buchheit KM, Vukovic M, Deb C, Wadsworth MH, Hughes TK, Kazer SW, Yoshimoto E, Cahill KN, Bhattacharyya N, Katz HR, Berger B, Laidlaw TM, et al. Allergic inflammatory memory in human respiratory epithelial progenitor cells. Nature. PMID 30135581 DOI: 10.1038/S41586-018-0449-8  0.234
1997 Jesurum CE, Pulimt V, Hobbs LW, Berger B. Modeling Collision Cascade Structure of SiO 2 , Si 3 N 4 and SiC using Local Topological Approaches Mrs Proceedings. 504: 39. DOI: 10.1557/Proc-504-39  0.234
2016 Nazeen S, Palmer NP, Berger B, Kohane IS. Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities. Genome Biology. 17: 228. PMID 27842596 DOI: 10.1186/S13059-016-1084-Z  0.23
2023 Sadhuka S, Fridman D, Berger B, Cho H. Assessing transcriptomic reidentification risks using discriminative sequence models. Genome Research. PMID 37541758 DOI: 10.1101/gr.277699.123  0.229
2020 Zhong E, Bepler T, Berger B, Davis J. CryoDRGN: Deep Generative Models for Reconstructing Heterogeneous 3D Structures from Cryo-electron Micrographs Microscopy and Microanalysis. 1-2. DOI: 10.1017/S1431927620019492  0.229
2019 Simmons S, Berger B, Sahinalp C. Protecting Genomic Data Privacy with Probabilistic Modeling. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 24: 403-414. PMID 30864341  0.228
2017 Fogg CN, Kovats DE, Berger B. 2017 ISCB Accomplishment by a Senior Scientist Award given to Pavel Pevzner. Plos Computational Biology. 13: e1005561. PMID 28665953 DOI: 10.1371/Journal.Pcbi.1005561  0.225
1990 Berger B, Rompel J. A better performance guarantee for approximate graph coloring Algorithmica. 5: 459-466. DOI: 10.1007/Bf01840398  0.225
2014 Pickrell JK, Patterson N, Loh PR, Lipson M, Berger B, Stoneking M, Pakendorf B, Reich D. Ancient west Eurasian ancestry in southern and eastern Africa. Proceedings of the National Academy of Sciences of the United States of America. 111: 2632-7. PMID 24550290 DOI: 10.1073/Pnas.1313787111  0.224
2019 Simmons S, Berger B, Sahinalp C. Protecting Genomic Data Privacy with Probabilistic Modeling. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 24: 403-414. PMID 30963078  0.224
2015 Berger E, Yorukoglu D, Berger B. HapTree-X: An Integrative Bayesian Framework for Haplotype Reconstruction from Transcriptome and Genome Sequencing Data. Research in Computational Molecular Biology : ... Annual International Conference, Recomb ... : Proceedings. Recomb (Conference : 2005-). 9029: 28-29. PMID 28825061 DOI: 10.1007/978-3-319-16706-0_4  0.223
2007 Wieland SC, Brownstein JS, Berger B, Mandl KD. Density-equalizing Euclidean minimum spanning trees for the detection of all disease cluster shapes. Proceedings of the National Academy of Sciences of the United States of America. 104: 9404-9. PMID 17519338 DOI: 10.1073/Pnas.0609457104  0.223
2017 Fogg CN, Kovats DE, Berger B. Message from the ISCB: 2017 ISCB Accomplishment by a Senior Scientist Award Given to Pavel Pevzner. Bioinformatics (Oxford, England). PMID 28605489 DOI: 10.1093/Bioinformatics/Btx289  0.22
2012 Palmer NP, Schmid PR, Berger B, Kohane IS. A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers. Genome Biology. 13: R71. PMID 22909066 DOI: 10.1186/Gb-2012-13-8-R71  0.219
2018 Pessia A, Corander J, Berger B. Kpax3: Bayesian bi-clustering of large sequence datasets. Bioinformatics (Oxford, England). PMID 29425273 DOI: 10.1093/Bioinformatics/Bty056  0.217
1995 Berger B, Brady M, Brown D, Leighton T. Nearly optimal algorithms and bounds for multilayer channel routing Journal of the Acm. 42: 500-542. DOI: 10.1145/201019.201037  0.217
2011 O'Donnell CW, Waldispühl J, Lis M, Halfmann R, Devadas S, Lindquist S, Berger B. A method for probing the mutational landscape of amyloid structure Bioinformatics. 27: i34-i42. PMID 21685090 DOI: 10.1093/bioinformatics/btr238  0.215
2021 Wu AP, Peng J, Berger B, Cho H. Bayesian information sharing enhances detection of regulatory associations in rare cell types. Bioinformatics (Oxford, England). 37: i349-i357. PMID 34252956 DOI: 10.1093/bioinformatics/btab269  0.215
2023 Jing B, Erives E, Pao-Huang P, Corso G, Berger B, Jaakkola T. EigenFold: Generative Protein Structure Prediction with Diffusion Models. Arxiv. PMID 37064532  0.214
2018 Anil A, Spalinskas R, Åkerborg Ö, Sahlén P, Berger B. HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications. Bioinformatics (Oxford, England). 34: 675-677. PMID 29444232 DOI: 10.1093/bioinformatics/btx625  0.214
2016 Amit I, Baker D, Barker R, Berger B, Bertozzi C, Bhatia S, Biffi A, Demichelis F, Doudna J, Dowdy SF, Endy D, Helmstaedter M, Junca H, June C, Kamb S, et al. Voices of biotech. Nature Biotechnology. 34: 270-275. PMID 26963549 DOI: 10.1038/Nbt.3502  0.214
2017 Fogg CN, Kovats DE, Berger B. Message from the ISCB: 2017 Outstanding Contributions to ISCB Award Given to Fran Lewitter. Bioinformatics (Oxford, England). PMID 28605497 DOI: 10.1093/Bioinformatics/Btx291  0.213
2010 Chindelevitch L, Liao CS, Berger B. Local optimization for global alignment of protein interaction networks. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 123-32. PMID 19908365  0.211
2017 Khurana V, Peng J, Chung CY, Auluck PK, Fanning S, Tardiff DF, Bartels T, Koeva M, Eichhorn SW, Benyamini H, Lou Y, Nutter-Upham A, Baru V, Freyzon Y, Tuncbag N, ... ... Berger B, et al. Genome-Scale Networks Link Neurodegenerative Disease Genes to α-Synuclein through Specific Molecular Pathways. Cell Systems. PMID 28131822 DOI: 10.1016/J.Cels.2016.12.011  0.211
2018 Cho H, Berger B, Peng J, Galitzine C, Vitek O, Beltran PMJ, Cristea IM, Görtler F, Solbrig S, Wettig T, Oefner PJ, Spang R, Altenbuchinger M, Basso RS, Hochbaum D, et al. Principles of Systems Biology, No. 31. Cell Systems. 7: 133-135. PMID 30138580 DOI: 10.1016/J.Cels.2018.08.005  0.21
2017 Fogg CN, Kovats DE, Berger B. 2017 Outstanding Contributions to ISCB Award: Fran Lewitter. Plos Computational Biology. 13: e1005560. PMID 28665935 DOI: 10.1371/Journal.Pcbi.1005560  0.209
2012 Levin A, Lis M, Ponty Y, O'Donnell CW, Devadas S, Berger B, Waldispühl J. A global sampling approach to designing and reengineering RNA secondary structures. Nucleic Acids Research. 40: 10041-52. PMID 22941632 DOI: 10.1093/nar/gks768  0.207
2021 Froelicher D, Troncoso-Pastoriza JR, Raisaro JL, Cuendet MA, Sousa JS, Cho H, Berger B, Fellay J, Hubaux JP. Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption. Nature Communications. 12: 5910. PMID 34635645 DOI: 10.1038/s41467-021-25972-y  0.206
2015 Yu YW, Yorukoglu D, Peng J, Berger B. Quality score compression improves genotyping accuracy. Nature Biotechnology. 33: 240-3. PMID 25748910 DOI: 10.1038/Nbt.3170  0.204
2019 Bepler T, Morin A, Rapp M, Brasch J, Shapiro L, Noble AJ, Berger B. TOPAZ: A Positive-Unlabeled Convolutional Neural Network CryoEM Particle Picker that can Pick Any Size and Shape Particle Microscopy and Microanalysis. 25: 986-987. DOI: 10.1017/S143192761900566X  0.202
2007 Pulim V, Bienkowska J, Berger B. LTHREADER: prediction of ligand-receptor interactions using localized threading. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 64-75. PMID 17992745  0.201
2022 Kinman LF, Powell BM, Zhong ED, Berger B, Davis JH. Uncovering structural ensembles from single-particle cryo-EM data using cryoDRGN. Nature Protocols. PMID 36376590 DOI: 10.1038/s41596-022-00763-x  0.2
2017 Fogg CN, Kovats DE, Berger B. Message from the ISCB: 2017 ISCB Innovator Award Given to Aviv Regev. Bioinformatics (Oxford, England). 33: 2243-2244. PMID 28881960 DOI: 10.1093/Bioinformatics/Btx288  0.199
2014 Yu YW, Yorukoglu D, Berger B. Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification. Research in Computational Molecular Biology : ... Annual International Conference, Recomb ... : Proceedings. Recomb (Conference : 2005-). 8394: 385-399. PMID 28825060 DOI: 10.1007/978-3-319-05269-4_31  0.195
2022 Jivanjee T, Ibrahim S, Nyquist SK, Gatter GJ, Bromley JD, Jaiswal S, Berger B, Behar SM, Love JC, Shalek AK. Enriching and Characterizing T Cell Repertoires from 3' Barcoded Single-Cell Whole Transcriptome Amplification Products. Methods in Molecular Biology (Clifton, N.J.). 2574: 159-182. PMID 36087201 DOI: 10.1007/978-1-0716-2712-9_7  0.192
2005 Xu J, Jiao F, Berger B. A tree-decomposition approach to protein structure prediction. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 247-56. PMID 16447982 DOI: 10.1109/CSB.2005.9  0.191
2018 Vetrovský T, Baldrian P, Morais D, Berger B. SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses. Bioinformatics (Oxford, England). PMID 29452334 DOI: 10.1093/Bioinformatics/Bty071  0.19
2021 Mishra D, Bepler T, Teague B, Berger B, Broach J, Weiss R. An engineered protein-phosphorylation toggle network with implications for endogenous network discovery. Science (New York, N.Y.). 373. PMID 34210851 DOI: 10.1126/science.aav0780  0.189
2022 Vasyliuk D, Felt J, Zhong ED, Berger B, Davis JH, Yip CK. Conformational landscape of the yeast SAGA complex as revealed by cryo-EM. Scientific Reports. 12: 12306. PMID 35853968 DOI: 10.1038/s41598-022-16391-0  0.189
2023 Otto JE, Ursu O, Wu AP, Winter EB, Cuoco MS, Ma S, Qian K, Michel BC, Buenrostro JD, Berger B, Regev A, Kadoch C. Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens. Molecular Cell. PMID 37028419 DOI: 10.1016/j.molcel.2023.03.013  0.188
2023 Jing B, Jaakkola T, Berger B. Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms. Arxiv. PMID 38106455  0.183
2021 Shajii A, Numanagić I, Leighton AT, Greenyer H, Amarasinghe S, Berger B. A Python-based programming language for high-performance computational genomics. Nature Biotechnology. PMID 34282326 DOI: 10.1038/s41587-021-00985-6  0.181
2012 Berger B. ISMB 2012 Proceedings Papers Committee. July 15 to July 19, 2012, Long Beach, CA, USA. Editorial. Bioinformatics (Oxford, England). 28: i1. PMID 22689748 DOI: 10.1093/Bioinformatics/Bts281  0.179
2023 Kim Y, Worby CJ, Acharya S, van Dijk LR, Alfonsetti D, Gromko Z, Azimzadeh P, Dodson K, Gerber G, Hultgren S, Earl AM, Berger B, Gibson TE. Strain Tracking with Uncertainty Quantification. Biorxiv : the Preprint Server For Biology. PMID 36747646 DOI: 10.1101/2023.01.25.525531  0.179
2007 Sontag D, Singh R, Berger B. Probabilistic modeling of systematic errors in two-hybrid experiments. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 445-57. PMID 17990509  0.179
2022 Sherman MA, Yaari AU, Priebe O, Dietlein F, Loh PR, Berger B. Genome-wide mapping of somatic mutation rates uncovers drivers of cancer. Nature Biotechnology. PMID 35726091 DOI: 10.1038/s41587-022-01353-8  0.178
2017 Fogg CN, Kovats DE, Berger B. 2017 ISCB Innovator Award: Aviv Regev. Plos Computational Biology. 13: e1005558. PMID 28665936 DOI: 10.1371/Journal.Pcbi.1005558  0.177
2017 Orenstein Y, Kim R, Fordyce P, Berger B. Joker de Bruijn: Sequence Libraries to Cover All -mers Using Joker Characters. Research in Computational Molecular Biology : ... Annual International Conference, Recomb ... : Proceedings. Recomb (Conference : 2005-). 10229: 389-390. PMID 29707702 DOI: 10.1007/978-3-319-56970-3  0.176
2023 Sledzieski S, Kshirsagar M, Baek M, Berger B, Dodhia R, Ferres JL. Democratizing Protein Language Models with Parameter-Efficient Fine-Tuning. Biorxiv : the Preprint Server For Biology. PMID 37986761 DOI: 10.1101/2023.11.09.566187  0.174
2021 Singh R, Hie BL, Narayan A, Berger B. Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalities. Genome Biology. 22: 131. PMID 33941239 DOI: 10.1186/s13059-021-02313-2  0.173
2017 Fogg CN, Kovats DE, Berger B. Message from the ISCB: 2017 ISCB Overton Prize Awarded to Christoph Bock. Bioinformatics (Oxford, England). PMID 28605508 DOI: 10.1093/Bioinformatics/Btx290  0.172
2015 Simmons S, Berger B. One Size Doesn't Fit All: Measuring Individual Privacy in Aggregate Genomic Data. Proceedings. Ieee Symposium On Security and Privacy. Workshops. 2015: 41-49. PMID 29202050 DOI: 10.1109/SPW.2015.25  0.17
2017 Fogg CN, Kovats DE, Berger B. 2017 ISCB Overton Prize awarded to Christoph Bock. Plos Computational Biology. 13: e1005559. PMID 28665945 DOI: 10.1371/Journal.Pcbi.1005559  0.17
2023 Ewen-Campen B, Luan H, Xu J, Singh R, Joshi N, Thakkar T, Berger B, White BH, Perrimon N. split-intein Gal4 provides intersectional genetic labeling that is fully repressible by Gal80. Biorxiv : the Preprint Server For Biology. PMID 36993523 DOI: 10.1101/2023.03.24.534001  0.166
2018 Pratapa A, Adames N, Kraikivski P, Franzese N, Tyson JJ, Peccoud J, Murali TM, Berger B. CrossPlan: Systematic Planning of Genetic Crosses to Validate Mathematical Models. Bioinformatics (Oxford, England). PMID 29432533 DOI: 10.1093/Bioinformatics/Bty072  0.166
2018 Hie B, Cho H, Berger B. Realizing private and practical pharmacological collaboration. Science (New York, N.Y.). 362: 347-350. PMID 30337410 DOI: 10.1126/science.aat4807  0.163
2023 Ewen-Campen B, Luan H, Xu J, Singh R, Joshi N, Thakkar T, Berger B, White BH, Perrimon N. split-intein Gal4 provides intersectional genetic labeling that is repressible by Gal80. Proceedings of the National Academy of Sciences of the United States of America. 120: e2304730120. PMID 37276389 DOI: 10.1073/pnas.2304730120  0.163
2020 Hie B, Bryson BD, Berger B. Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design. Cell Systems. 11: 461-477.e9. PMID 33065027 DOI: 10.1016/j.cels.2020.09.007  0.162
2023 Smajlović H, Shajii A, Berger B, Cho H, Numanagić I. Sequre: a high-performance framework for secure multiparty computation enables biomedical data sharing. Genome Biology. 24: 5. PMID 36631897 DOI: 10.1186/s13059-022-02841-5  0.162
2022 Duffy EE, Finander B, Choi G, Carter AC, Pritisanac I, Alam A, Luria V, Karger A, Phu W, Sherman MA, Assad EG, Pajarillo N, Khitun A, Crouch EE, Ganesh S, ... ... Berger B, et al. Developmental dynamics of RNA translation in the human brain. Nature Neuroscience. PMID 36171426 DOI: 10.1038/s41593-022-01164-9  0.156
2018 Pandey P, Bender MA, Johnson R, Patro R, Berger B. Squeakr: an exact and approximate k-mer counting system. Bioinformatics (Oxford, England). 34: 568-575. PMID 29444235 DOI: 10.1093/Bioinformatics/Btx636  0.153
2021 Zhong ED, Bepler T, Berger B, Davis JH. CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks. Nature Methods. 18: 176-185. PMID 33542510 DOI: 10.1038/s41592-020-01049-4  0.149
2023 DeMeo B, Berger B. SCA: recovering single-cell heterogeneity through information-based dimensionality reduction. Genome Biology. 24: 195. PMID 37626411 DOI: 10.1186/s13059-023-02998-7  0.142
2021 Narayan A, Berger B, Cho H. Assessing single-cell transcriptomic variability through density-preserving data visualization. Nature Biotechnology. PMID 33462509 DOI: 10.1038/s41587-020-00801-7  0.134
2020 Bepler T, Kelley K, Noble AJ, Berger B. Topaz-Denoise: general deep denoising models for cryoEM and cryoET. Nature Communications. 11: 5208. PMID 33060581 DOI: 10.1038/s41467-020-18952-1  0.131
2023 Virshup I, Bredikhin D, Heumos L, Palla G, Sturm G, Gayoso A, Kats I, Koutrouli M, Berger B, Pe'er D, Regev A, Teichmann SA, Finotello F, Wolf FA, Yosef N, et al. The scverse project provides a computational ecosystem for single-cell omics data analysis. Nature Biotechnology. PMID 37037904 DOI: 10.1038/s41587-023-01733-8  0.128
2021 Hie B, Zhong ED, Berger B, Bryson B. Learning the language of viral evolution and escape. Science (New York, N.Y.). 371: 284-288. PMID 33446556 DOI: 10.1126/science.abd7331  0.126
2019 Cho H, DeMeo B, Peng J, Berger B. Large-Margin Classification in Hyperbolic Space. Proceedings of Machine Learning Research. 89: 1832-1840. PMID 32832915  0.122
2024 Singh R, Wu AP, Mudide A, Berger B. Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors. Cell Systems. 15: 462-474.e5. PMID 38754366 DOI: 10.1016/j.cels.2024.04.005  0.12
2024 Kshirsagar M, Meller A, Humphreys I, Sledzieski S, Xu Y, Dodhia R, Horvitz E, Berger B, Bowman G, Ferres JL, Baker D, Baek M. Rapid and accurate prediction of protein homo-oligomer symmetry with Seq2Symm. Research Square. PMID 38746169 DOI: 10.21203/rs.3.rs-4215086/v1  0.12
2023 Froelicher D, Cho H, Edupalli M, Sousa JS, Bossuat JP, Pyrgelis A, Troncoso-Pastoriza JR, Berger B, Hubaux JP. Scalable and Privacy-Preserving Federated Principal Component Analysis. Proceedings. Ieee Symposium On Security and Privacy. 2023: 1908-1925. PMID 38665901 DOI: 10.1109/sp46215.2023.10179350  0.12
2022 Gideon HP, Hughes TK, Tzouanas CN, Wadsworth MH, Tu AA, Gierahn TM, Peters JM, Hopkins FF, Wei JR, Kummerlowe C, Grant NL, Nargan K, Phuah JY, Borish HJ, Maiello P, ... ... Berger B, et al. Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control. Immunity. PMID 35483355 DOI: 10.1016/j.immuni.2022.04.004  0.11
2018 Shajii A, Numanagić I, Berger B. Latent Variable Model for Aligning Barcoded Short-Reads Improves Downstream Analyses. Research in Computational Molecular Biology : ... Annual International Conference, Recomb ... : Proceedings. Recomb (Conference : 2005-). 10812: 280-282. PMID 29888346  0.109
2014 Tucker G, Price AL, Berger B. Improving the power of GWAS and avoiding confounding from population stratification with PC-Select. Genetics. 197: 1045-9. PMID 24788602 DOI: 10.1534/genetics.114.164285  0.108
2022 Jaiswal S, Nyquist SK, Boyce S, Jivanjee T, Ibrahim S, Bromley JD, Gatter GJ, Gideon H, Patel K, Ganchua SK, Berger B, Fortune SM, Flynn JL, Shalek AK, Behar SM. Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis). Bmc Genomics. 23: 647. PMID 36096729 DOI: 10.1186/s12864-022-08867-0  0.104
2022 Shan S, Luo S, Yang Z, Hong J, Su Y, Ding F, Fu L, Li C, Chen P, Ma J, Shi X, Zhang Q, Berger B, Zhang L, Peng J. Deep learning guided optimization of human antibody against SARS-CoV-2 variants with broad neutralization. Proceedings of the National Academy of Sciences of the United States of America. 119: e2122954119. PMID 35238654 DOI: 10.1073/pnas.2122954119  0.104
2020 Gui M, Ma M, Sze-Tu E, Wang X, Koh F, Zhong ED, Berger B, Davis JH, Dutcher SK, Zhang R, Brown A. Structures of radial spokes and associated complexes important for ciliary motility. Nature Structural & Molecular Biology. PMID 33318703 DOI: 10.1038/s41594-020-00530-0  0.102
2015 Cho H, Berger B, Peng J. Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks. Research in Computational Molecular Biology : ... Annual International Conference, Recomb ... : Proceedings. Recomb (Conference : 2005-). 9029: 62-64. PMID 28748230 DOI: 10.1007/978-3-319-16706-0_9  0.1
2008 Davidzon G, Pankey E, Loudon T, Schmid P, Berger B, Berkowicz D. SemanticDx: a prototype to facilitate use of biostatistics at the point-of-care. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 921. PMID 18999188  0.098
2021 Dwyer DF, Ordovas-Montanes J, Allon SJ, Buchheit KM, Vukovic M, Derakhshan T, Feng C, Lai J, Hughes TK, Nyquist SK, Giannetti MP, Berger B, Bhattacharyya N, Roditi RE, Katz HR, et al. Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation. Science Immunology. 6. PMID 33637594 DOI: 10.1126/sciimmunol.abb7221  0.096
2021 Sherman MA, Rodin RE, Genovese G, Dias C, Barton AR, Mukamel RE, Berger B, Park PJ, Walsh CA, Loh PR. Large mosaic copy number variations confer autism risk. Nature Neuroscience. PMID 33432194 DOI: 10.1038/s41593-020-00766-5  0.086
2022 Maher MC, Bartha I, Weaver S, di Iulio J, Ferri E, Soriaga L, Lempp FA, Hie BL, Bryson B, Berger B, Robertson DL, Snell G, Corti D, Virgin HW, Kosakovsky Pond SL, et al. Predicting the mutational drivers of future SARS-CoV-2 variants of concern. Science Translational Medicine. eabk3445. PMID 35014856 DOI: 10.1126/scitranslmed.abk3445  0.086
2023 Kang J, Zhang C, Wang Y, Feng J, Berger B, Perrimon N, Shen J. Lipophorin Receptors Genetically Modulate Neurodegeneration Caused by Reduction of Psn Expression in the Aging Drosophila Brain. Genetics. PMID 37996068 DOI: 10.1093/genetics/iyad202  0.085
2022 Berger B, Tian D, Li WV, El-Kebir M, Tomescu AI, Singh R, Beerenwinkel N, Li Y, Boucher C, Bar-Joseph Z. What are the keys to succeeding as a computational biologist in today's research climate? Cell Systems. 13: 781-785. PMID 36265464 DOI: 10.1016/j.cels.2022.09.005  0.081
2022 Smajlović H, Shajii A, Berger B, Cho H, Numanagić I. Sequre: a high-performance framework for rapid development of secure bioinformatics pipelines. Ieee International Symposium On Parallel & Distributed Processing, Workshops and Phd Forum : [Proceedings]. Ieee International Symposium On Parallel & Distributed Processing, Workshops and Phd Forum. 2022: 164-165. PMID 35958356  0.068
2022 Nyquist SK, Gao P, Haining TKJ, Retchin MR, Golan Y, Drake RS, Kolb K, Mead BE, Ahituv N, Martinez ME, Shalek AK, Berger B, Goods BA. Cellular and transcriptional diversity over the course of human lactation. Proceedings of the National Academy of Sciences of the United States of America. 119: e2121720119. PMID 35377806 DOI: 10.1073/pnas.2121720119  0.06
2023 Bromley JD, Ganchua SKC, Nyquist SK, Maiello P, Chao M, Borish HJ, Rodgers M, Tomko J, Kracinovsky K, Mugahid D, Nguyen S, Wang D, Rosenberg JM, Klein EC, Gideon HP, ... ... Berger B, et al. CD4 T cells are homeostatic regulators during reinfection. Biorxiv : the Preprint Server For Biology. PMID 38187598 DOI: 10.1101/2023.12.20.572669  0.058
2018 Cho H, Berger B, Peng J. Generalizable visualization of mega-scale single-cell data. Research in Computational Molecular Biology : ... Annual International Conference, Recomb ... : Proceedings. Recomb (Conference : 2005-). 10812: 251-253. PMID 29725668  0.058
2019 Shajii A, Numanagić I, Baghdadi R, Berger B, Amarasinghe S. Seq: A High-Performance Language for Bioinformatics. Proceedings of the Acm On Programming Languages. 3. PMID 35775031 DOI: 10.1145/3360551  0.057
2019 Shajii A, Numanagić I, Baghdadi R, Berger B, Amarasinghe S. Seq: A High-Performance Language for Bioinformatics. Proceedings of the Acm On Programming Languages. 3. PMID 35775031 DOI: 10.1145/3360551  0.057
2021 Fardoos R, Asowata OE, Herbert N, Nyquist SK, Zungu Y, Singh A, Ngoepe A, Mbano IM, Mthabela N, Ramjit D, Karim F, Kuhn W, Madela FG, Manzini VT, Anderson F, ... Berger B, et al. HIV infection drives interferon signalling within intestinal SARS-CoV-2 target cells. Jci Insight. PMID 34252054 DOI: 10.1172/jci.insight.148920  0.052
2023 Winchell CG, Nyquist SK, Chao MC, Maiello P, Myers AJ, Hopkins F, Chase M, Gideon HP, Patel KV, Bromley JD, Simonson AW, Floyd-O'Sullivan R, Wadsworth M, Rosenberg JM, Uddin R, ... ... Berger B, et al. CD8+ lymphocytes are critical for early control of tuberculosis in macaques. The Journal of Experimental Medicine. 220. PMID 37843832 DOI: 10.1084/jem.20230707  0.05
2018 Bepler T, Morin A, Noble AJ, Brasch J, Shapiro L, Berger B. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Research in Computational Molecular Biology : ... Annual International Conference, Recomb ... : Proceedings. Recomb (Conference : 2005-). 10812: 245-247. PMID 29707703  0.049
2022 Fardoos R, Nyquist SK, Asowata OE, Kazer SW, Singh A, Ngoepe A, Giandhari J, Mthabela N, Ramjit D, Singh S, Karim F, Buus S, Anderson F, Porterfield JZ, Sibiya AL, ... ... Berger B, et al. HIV specific CD8 T-like cells in tonsils express exhaustive signatures in the absence of natural HIV control. Frontiers in Immunology. 13: 912038. PMID 36330531 DOI: 10.3389/fimmu.2022.912038  0.049
2021 Froelicher D, Troncoso-Pastoriza JR, Raisaro JL, Cuendet MA, Sousa JS, Cho H, Berger B, Fellay J, Hubaux JP. Author Correction: Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption. Nature Communications. 12: 6649. PMID 34764286 DOI: 10.1038/s41467-021-26885-6  0.048
2016 Luo Y, Zeng J, Berger B, Peng J. Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning. Research in Computational Molecular Biology : ... Annual International Conference, Recomb ... : Proceedings. Recomb (Conference : 2005-). 9649: 255-257. PMID 28127592  0.048
2022 Bartos LJ, Meek GA, Berger BG. Effectiveness of Yoga versus Exercise for Reducing Falling Risk in Older Adults: Physical and Psychological Indices. Perceptual and Motor Skills. 315125221100820. PMID 35613041 DOI: 10.1177/00315125221100820  0.046
2022 Berger BG, Darby LA, Owen DR, Carels RA. "Feeling Good" After Exercise During a Weight Loss Program: Subjective Well-Being in Support of a Hedonic Paradigm. Perceptual and Motor Skills. 315125221130444. PMID 36176046 DOI: 10.1177/00315125221130444  0.036
2006 Carels RA, Berger B, Darby L. The association between mood states and physical activity in postmenopausal, obese, sedentary women. Journal of Aging and Physical Activity. 14: 12-28. PMID 16648649 DOI: 10.1123/Japa.14.1.12  0.033
2016 Darby LA, Berger BG, Owen DR. Senior Golfers - Fitness, Mood and Enjoyment Measured Before and After Golf-Specific Training: A Pilot Study: 171 Board #8 June 1, 9: 30 AM - 11: 00 AM. Medicine and Science in Sports and Exercise. 48: 31. PMID 27359426 DOI: 10.1249/01.mss.0000485102.01688.fd  0.031
2007 Carels RA, Coit C, Young K, Berger B. Exercise makes you feel good, but does feeling good make you exercise?: an examination of obese dieters. Journal of Sport & Exercise Psychology. 29: 706-22. PMID 18089900 DOI: 10.1123/Jsep.29.6.706  0.015
2016 Tobar DA, Kaus RJ, Berger BG. Neuroticism And Gender On Affect And Feelings During And After A Crossfit Workout: 2523 Board #46 June 3, 11: 00 AM - 12: 30 PM. Medicine and Science in Sports and Exercise. 48: 696. PMID 27361159 DOI: 10.1249/01.mss.0000487092.88699.27  0.01
Hide low-probability matches.