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Computational Solutions for "Omics Data" |
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Bonnie
Berger, Jian Peng and Mona Singh |
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Nature Reviews
Genetics, 14 (2013): 333-346 |
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| 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. |
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http://www.nature.com/nrg/journal/v14/n5/abs/nrg3433.html |
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Inferring admixture histories of human populations using
linkage disequilibrium |
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Po-Ru
Loh, Mark Lipson, Nick Patterson, Priya Moorjani, Joseph K.
Pickrell, David Reich and Bonnie Berger |
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Genetics,
Mon, 1 Apr 2013 13:03:15
-0400 |
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| 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. |
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http://www.genetics.org/content/193/4.cover-expansion |
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Making sense out of massive data by
going beyond differential gene expression |
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Patrick Schmid, Nathan Palmer, Issac
Kohane and Bonnie Berger * |
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Proceedings of the National Academy
of Sciences 109 (2012) no. 15:5549-5906 |
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| Introduces Concordia
http://www.pnas.org/content/early/2012/03/21/1118792109, 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
http://genomebiology.com/2012/13/8/R71
shows tumor samples acquire stem-cell-like expression programming. |
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http://www.pnas.org/content/early/2012/03/21/1118792109 |
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Conserved microRNA targeting in drosophila is as widespread
in coding regions as in 3' UTRs |
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Michael Schnall-Levin, Yong Zhao, Norbert Perrimon and Bonnie Berger
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Proceedings of the National Academy of Sciences (2010) 107:36, 15751-15756 |
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Developed a tool, MinoTar, for predicting microRNA targets in Open Reading Frames (ORFS). In a companion Genome Research paper,
http://genome.cshlp.org/content/early/2011/06/16/gr.121210.111?top=1,
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 |
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Lenore Cowen, Matt Menke and Bonnie Berger
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| PLoS Computational Biology
(2008)
4, Issue 1. |
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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.
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http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0040010 |
| IsoRank:
Global alignment of multiple protein interaction networks with
applications to functional orthology detection |
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| Rohit Singh, Jinbo Xu and Bonnie Berger |
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| Proceedings of the National Academy of Sciences (2008) 105:35, 12763-12768. |
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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. |
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http://www.pnas.org/content/105/35/12763.full |
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Methods in
comparative genomics: genome correspondence, gene identification, and motif
discovery
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| Manolis Kellis, Nick Patterson, Bruce Birren, Bonnie Berger , and Eric S. Lander |
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Journal of Computational Biology (2004) 11 no.2-3, 319-355. |
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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.
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bibTeX citation |
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ARACHNE: A
whole-genome shotgun assembler |
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| | Serafim Batzoglou
, David B. Jaffe
, Ken Stanley
, Jonathan Butler
, Sante Gnerre
, Evan Mauceli
, Bonnie Berger
, Jill P. Mesirov
, and Eric S. Lander
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| | Genome Research
(2002
) 12 no. 1, 177
-189.
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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. |
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abstract |
bibTeX citation |
publisher's site |
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Human and
mouse gene structure: comparative analysis and application to exon prediction |
|
| | Serafim Batzoglou, Lior Pachter, Jill Mesirov, Bonnie Berger, and Eric S. Lander
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| | Genome Research (2000) 10, 950-958.
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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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abstract |
bibTeX citation |
publisher's site |
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Protein
folding in the hydrophobic-hydrophilic (HP) model is NP-complete |
|
| | Bonnie Berger and Tom Leighton
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| | Journal of Computational Biology (1998) 5 no. 1, 27-40.
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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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abstract |
bibTeX citation |
publisher's site |
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MultiCoil: A
program for predicting two and three stranded coiled coils
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|
| | Ethan Wolf, Peter S. Kim, and Bonnie Berger
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| | Protein Science (1997) 6 no. 6, 1179-1189.
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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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abstract |
bibTeX citation |
publisher's site |
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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
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| | Proceedings of the National Academy of Science USA (1995) 92, 8259-8263.
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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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abstract |
bibTeX citation |
publisher's site |
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A local
rule based theory of virus shell assembly |
|
| | Bonnie Berger, Peter W. Shor, Lisa Tucker-Kellogg, and Jonathan King
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| | Proceedings of the National Academy of Science USA (1994) 91 no. 16, 7732-7736.
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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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abstract |
bibTeX citation |
publisher's site |
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Simulating (logc n)-wise
independence in NC
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| | Bonnie Berger and John Rompel
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| | Journal of the Association for Computing Machinery (1991) 38 no. 4, 1026-1046.
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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.
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abstract |
bibTeX citation |
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