Bonnie Berger

  Berger Publications
Selected Publications List - All Publications
Computational Solutions for "Omics Data"
Bonnie Berger, Jian Peng and Mona Singh
Nature Reviews Genetics, 14 (2013): 333-346
Samples the algorithmic landscape, focusing on state-of-the-art techniques, the understanding of which will aid the bench biologist in analysing omics data. Spotlights specific examples that have facilitated and enriched analyses of sequence, transcriptomic and network data sets.

Inferring admixture histories of human populations using linkage disequilibrium
Po-Ru Loh, Mark Lipson, Nick Patterson, Priya Moorjani, Joseph K. Pickrell, David Reich and Bonnie Berger
Genetics, Mon, 1 Apr 2013 13:03:15 -0400
Develop a sophisticated statistical framework for admixture inference and clever algorithmic techniques to speed up such analysis by three orders of magnitude; these methods are already being used.

Compressive Genomics
Po-Ru Loh, Michael Baym and Bonnie Berger
Nature Biotechnology 30 (2012) 927-930 Published online 10 July 2012
Algorithms that compute directly on compressed genomic data allow analyses to keep pace with data generation.

Making sense out of massive data by going beyond differential gene expression
Patrick Schmid, Nathan Palmer, Issac Kohane and Bonnie Berger *
Proceedings of the National Academy of Sciences 109 (2012) no. 15:5549-5906
Introduces Concordia, which  generates a ranked list of marker genes for a given complex pheno­type by querying a large-scale gene expression database sorted by gene expression intensity for each pheno­type. Concordia is able to classify tissue types with a high degree of accuracy, such as metastasized tumor samples, which strikingly resemble their tissue of ori­gin. A companion paper in Genome Biology shows tumor samples acquire stem-cell-like expression programming.

Conserved microRNA targeting in drosophila is as widespread in coding regions as in 3' UTRs
Michael Schnall-Levin, Yong Zhao, Norbert Perrimon and Bonnie Berger
Proceedings of the National Academy of Sciences (2010) 107:36, 15751-15756
Developed a tool, MinoTar, for predicting microRNA targets in Open Reading Frames (ORFS). In a companion Genome Research paper,, discover a phenomenon where sequence repeats lead to striking numbers of miRNA ORF target sites, demonstrating a class of previously overlooked miRNA targets and a novel role for sequence repeats in regulation. 70 combined citations.

Matt: Local flexibility aids protein multiple structure alignment
Lenore Cowen, Matt Menke and Bonnie Berger
PLoS Computational Biology (2008) 4, Issue 1.
Perform multiple protein structure alignment by innovatively allowing the structures to freely move while they are being aligned and then pastes them back together according to steric constraints; the Matt program has been termed the "most accurate" of its kind by an independent review (Berbalk et al., Protein Science, 2009); 78 citations.

IsoRank: Global alignment of multiple protein interaction networks with applications to functional orthology detection
Rohit Singh, Jinbo Xu and Bonnie Berger
Proceedings of the National Academy of Sciences (2008) 105:35, 12763-12768.   

Introduces global network alignment algorithm Isorank (later IsorankN), simultaneously incorporating both sequence and network data to map proteins across species, and pioneered the use of spectral methods to solve this problem. Led to IsoBase, a database of functionally-related proteins, which allows biologists to map proteins across model organisms; over 373 combined citations.

  Methods in comparative genomics: genome correspondence, gene identification, and motif discovery
Manolis Kellis, Nick Patterson, Bruce Birren, Bonnie Berger , and Eric S. Lander
Journal of Computational Biology (2004) 11 no.2-3, 319-355.
Ground breaking work on comparative genomics of entire closely-related genomes, and to identify genes and regulatory motifs; computational underpinnings of Nature (2004) paper. Over 1300 combined citations.

 bibTeX citation

  ARACHNE: A whole-genome shotgun assembler
 Serafim Batzoglou , David B. Jaffe , Ken Stanley , Jonathan Butler , Sante Gnerre , Evan Mauceli , Bonnie Berger , Jill P. Mesirov , and Eric S. Lander
 Genome Research (2002 ) 12 no. 1, 177 -189.

Seminal program for whole genome shotgun assembly; used extensively by the Whitehead & Broad Institutes and other labs for shotgun sequencing of the human genome; over 415 citations and 657 combined citations with the sequel program.

abstract  bibTeX citation publisher's site

  Human and mouse gene structure: comparative analysis and application to exon prediction
 Serafim Batzoglou, Lior Pachter, Jill Mesirov, Bonnie Berger, and Eric S. Lander
 Genome Research (2000) 10, 950-958.

Ground-breaking work on comparative genomics of entire genomes and to predict genes; over 375 citations. Led to first work on comparative genomics of entire closely-related genomes, and to identify genes and regulatory motifs in companion J. of Computational Biology 2004 and Nature 2004 articles; over 1700 combined citations.

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  Protein folding in the hydrophobic-hydrophilic (HP) model is NP-complete
 Bonnie Berger and Tom Leighton
 Journal of Computational Biology (1998) 5 no. 1, 27-40.
Show that the most widely-studied theoretical formulation of protein folding-folding in the hydrophobic-polar lattice model-is NP-complete; many previous papers only were able to show complexity results for limited versions of the problem and not succeeding for the widely-studied case; over 340 citations. Received Test of Time Award at RECOMB 2010.
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  MultiCoil: A program for predicting two and three stranded coiled coils
 Ethan Wolf, Peter S. Kim, and Bonnie Berger
 Protein Science (1997) 6 no. 6, 1179-1189.
First paper to accurately predict oligomerization state of coiled coils using pairwise residue correlations and clustering in higher dimensional space; over 500 citations.
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  Predicting coiled coils by use of pairwise residue correlations
 Bonnie Berger, David B. Wilson, Ethan Wolf, Theodore Tonchev, Maria Milla, and Peter S. Kim
 Proceedings of the National Academy of Science USA (1995) 92, 8259-8263.

Introduces probabilistic modeling of residue interactions for protein fold recognition, and in particular to predict coiled coils in Paircoil suite of programs; also accurately predict coiled-coil oligomerization states and viral propensity in sequel Multicoil, Multicoil2, and Learncoil suite. These programs have been used to make important biological discoveries, including implicating coiled-coils in the membrane fusion mechanism for large classes of viruses and informed development of inhibitory drugs for HIV through Dr. Peter S. Kim at Merck. Over 1700 combined citations.

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  A local rule based theory of virus shell assembly
 Bonnie Berger, Peter W. Shor, Lisa Tucker-Kellogg, and Jonathan King
 Proceedings of the National Academy of Science USA (1994) 91 no. 16, 7732-7736.

Shows that the self-assembly and mis-assembly of viral shells–though seemingly a complex procedure–can be explained purely by local rules that specify the assembly of the desired structure by limiting the combinatorial space of all possible arrangements; over 320 combined virus shell assembly citations to this work. This paper also led to an application of similar approaches in materials science engineering by Berger, Hobbs and collaborators (over 200 citations) and a cascade of similar modeling in that field by Hobbs and others, which have had thousands of citations.

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  Simulating (logc n)-wise independence in NC
 Bonnie Berger and John Rompel
 Journal of the Association for Computing Machinery (1991) 38 no. 4, 1026-1046.
Remove randomness from parallel algorithms, demonstrating that we can efficiently solve important graph-theoretic problems that we show required only poly-logarithmic, rather than full or pairwise, independence of the random variables; over 100 citations.
abstract  bibTeX citation