Bonnie Berger - Publications

Affiliations: 
EECS Massachusetts Institute of Technology, Cambridge, MA, United States 

69 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, 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
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.6
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  0.6
2016 Simmons S, Berger B. Realizing Privacy Preserving Genome-wide Association Studies. Bioinformatics (Oxford, England). PMID 26769317 DOI: 10.1093/bioinformatics/btw009  0.6
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  0.32
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  0.6
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  0.6
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  0.6
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  0.6
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  0.32
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  0.6
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  0.32
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.32
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
2013 Berger B, Peng J, Singh M. Computational solutions for omics data. Nature Reviews. Genetics. 14: 333-46. PMID 23594911 DOI: 10.1038/nrg3433  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.56
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  0.6
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