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M Kloster

Publications and source records attributed to M Kloster.

6 recordsLinked to original sources
PubMed2004

Finding regulatory modules through large-scale gene-expression data analysis.

MOTIVATION: The use of gene microchips has enabled a rapid accumulation of gene-expression data. One of the major challenges of analyzing this data is the diversity, in both size and signal strength, of the various modules in the gene regulatory networks of organisms. RESULTS: Based on the iterative signature algorithm [Bergmann,S., Ihmels,J. and Barkai,N. (2002) Phys. Rev. E 67, 031902], we present an algorithm-the progressive iterative signature algorithm (PISA)-that, by sequentially eliminating modules, allows unsupervised identification of both large and small regulatory modules. We applied PISA to a large set of yeast gene-expression data, and, using the Gene Ontology database as a reference, found that the algorithm is much better able to identify regulatory modules than methods based on high-throughput transcription-factor binding experiments or on comparative genomics.

Algorithms↗
PubMed2001

Exact solution of a stochastic directed sandpile model.

We introduce and analytically solve a directed sandpile model with stochastic toppling rules. The model clearly belongs to a different universality class from its counterpart with deterministic toppling rules, previously solved by Dhar and Ramaswamy. The critical exponents are D(//)=7/4, tau=10/7 in two dimensions and D(//)=3/2, tau=4/3 in one dimension. The upper critical dimension of the model is three, at which the exponents apart from logarithmic corrections reach their mean-field values D(//)=2, tau=3/2.

Journal Article↗
PubMed1998

Sequence-dependent extrusion of a small DNA hairpin at the N4 virion RNA polymerase promoters.

Bacteriophage N4 virion RNA polymerase promoters contain five to seven-base inverted repeats separated by three bases and centered at position -12 from the site of transcription initiation. We have previously shown that these inverted repeats extrude as hairpins at physiological superhelical densities in a Mg(II)-dependent manner. Mg(II)-dependent hairpin extrusion at promoters P1 and P2 displays quantitative differences in reactivity to structural probes at different DNA superhelical densities, with extrusion at P2 being more favored at low superhelical density. Analyses of mutant promoters using structure-specific probes revealed that specific sequences, at the closing base-pair of the hairpin and at the loop (i.e. 5'-C-GXA-G-3' where X=G, A, T), are required for extrusion of the small promoter hairpins at physiological superhelical density. The sequence-dependent requirements for extrusion of the small N4 promoter hairpins may be generally applicable for other such sequences found both in prokaryotic and eukaryotic genomes.

Acetaldehyde↗