Piotr Berman
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Explore the profile of Piotr Berman including associated specialties, affiliations and a list of published articles.
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7
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8
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Recent Articles
1.
Jeong J, Berman P, Przytycka T
IEEE/ACM Trans Comput Biol Bioinform
. 2008 Nov;
5(4):484-91.
PMID: 18989036
The topology of beta-sheets is defined by the pattern of hydrogen-bonded strand pairing. Therefore, predicting hydrogen bonded strand partners is a fundamental step towards predicting beta-sheet topology. At the same...
2.
Jeong J, Berman P
BMC Syst Biol
. 2008 Feb;
2:12.
PMID: 18237406
Background: We investigate the cycles in the transcription network of Saccharomyces cerevisiae. Unlike a similar network of Escherichia coli, it contains many cycles. We characterize properties of these cycles and...
3.
Berman P, Dasgupta B, Sontag E
Ann N Y Acad Sci
. 2007 Oct;
1115:132-41.
PMID: 17925351
This paper studies a computational problem motivated by the modular response analysis method for reverse engineering of protein and gene networks. This set-cover problem is hard to solve exactly for...
4.
Jeong J, Berman P
Phys Rev E Stat Nonlin Soft Matter Phys
. 2007 May;
75(3 Pt 2):036104.
PMID: 17500756
We study local search algorithms for networks with heterogeneous edge weights, testing them on scale-free and Erdös-Rényi networks. We assume that the location of the destination node is discovered when...
5.
Hou M, Berman P, Hsu C, Harris R
Bioinformatics
. 2007 Feb;
23(8):917-25.
PMID: 17308341
Motivation: Complex genomes contain numerous repeated sequences, and genomic duplication is believed to be a main evolutionary mechanism to obtain new functions. Several tools are available for de novo repeat...
6.
Jeong J, Berman P, Przytycka T
BMC Struct Biol
. 2006 Mar;
6:3.
PMID: 16524467
Background: It has been proposed that secondary structure information can be used to classify (to some extend) protein folds. Since this method utilizes very limited information about the protein structure,...
7.
Berman P, Bertone P, Dasgupta B, Gerstein M, Kao M, Snyder M
J Comput Biol
. 2004 Dec;
11(4):766-85.
PMID: 15579244
In this paper, we consider several variations of the following basic tiling problem: given a sequence of real numbers with two size-bound parameters, we want to find a set of...