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3' untranslated regions (3' UTRs) contain binding sites for many regulatory elements, and in particular for microRNAs (miRNAs). The importance of miRNA-mediated post-transcriptional regulation has become increasingly clear in the last few years. We propose two complementary approaches to the statistical analysis of oligonucleotide frequencies in mammalian 3' UTRs aimed at the identification of candidate binding sites for regulatory elements. The first method is based on the identification of sets of genes characterized by evolutionarily conserved overrepresentation of an oligonucleotide. The second method is based on the identification of oligonucleotides showing statistically significant strand asymmetry in their distribution in 3' UTRs. Both methods are able to identify many previously known binding sites located in 3'UTRs, and in particular seed regions of known miRNAs. Many new candidates are proposed for experimental verification., Comment: Added two references

We discuss a simple and powerful approach for the ab initio identification of cis-regulatory motifs involved in transcriptional regulation. The method we present integrates several elements: human-mouse comparison, statistical analysis of genomic sequences and the concept of coregulation. We apply it to a complete scan of the human genome. By using the catalogue of conserved upstream sequences collected in the CORG database we construct sets of genes sharing the same overrepresented motif (short DNA sequence) in their upstream regions both in human and in mouse. We perform this construction for all possible motifs from 5 to 8 nucleotides in length and then filter the resulting sets looking for two types of evidence of coregulation: first, we analyze the Gene Ontology annotation of the genes in the set, searching for statistically significant common annotations; second, we analyze the expression profiles of the genes in the set as measured by microarray experiments, searching for evidence of coexpression. The sets which pass one or both filters are conjectured to contain a significant fraction of coregulated genes, and the upstream motifs characterizing the sets are thus good candidates to be the binding sites of the TF's involved in such regulation. In this way we find various known motifs and also some new candidate binding sites., Comment: 22 pages, 2 figures. Supplementary material available from the authors

BACKGROUND: Transcriptional regulation is a key mechanism in the functioning of the cell, and is mostly effected through transcription factors binding to specific recognition motifs located upstream of the coding region of the regulated gene. The computational identification of such motifs is made easier by the fact that they often appear several times in the upstream region of the regulated genes, so that the number of occurrences of relevant motifs is often significantly larger than expected by pure chance. RESULTS: To exploit this fact, we construct sets of genes characterized by the statistical overrepresentation of a certain motif in their upstream regions. Then we study the functional characterization of these sets by analyzing their annotation to Gene Ontology terms. For the sets showing a statistically significant specific functional characterization, we conjecture that the upstream motif characterizing the set is a binding site for a transcription factor involved in the regulation of the genes in the set. CONCLUSIONS: The method we propose is able to identify many known binding sites in S. cerevisiae and new candidate targets of regulation by known transcription factors. Its application to less well studied organisms is likely to be valuable in the exploration of their regulatory interaction network., Comment: 19 pages, 1 figure. Published version with several improvements. Supplementary material available from the authors

We study spatial networks constructed by randomly placing nodes on a manifold and joining two nodes with an edge whenever their distance is less than a certain cutoff. We derive the general expression for the connectivity distribution of such networks as a functional of the distribution of the nodes. We show that for regular spatial densities, the corresponding spatial network has a connectivity distribution decreasing faster than an exponential. In contrast, we also show that scale-free networks with a power law decreasing connectivity distribution are obtained when a certain information measure of the node distribution (integral of higher powers of the distribution) diverges. We illustrate our results on a simple example for which we present simulation results. Finally, we speculate on the role played by the limiting case P(k)=1/k which appears empirically to be relevant to spatial networks of biological origin such as the ones constructed from gene expression data., Comment: 6 pages, 1 figure

We study the spectrum of screening masses in the deconfined phase of (3+1)D SU(2) pure gauge theory near criticality and compare it with the spectrum of bound states in the broken symmetry phase of the 3D Ising model, which is related to the gauge theory by universality., Comment: 3 pages, uses espcrc2.sty, Lattice2002(nonzerot)

A new method is proposed for determining the critical indices of the deconfinement transition in gauge theories, based on the finite-size scaling analysis of simple lattice operators, such as the plaquette. A precise determination of the critical index $\nu$, in agreement with the prediction of the Svetitsky-Yaffe conjecture, is obtained for SU(3) gauge theory in (2+1)-dimension. Preliminary results for SU(2) in (3+1)-dimension are also given., Comment: poster at Lattice2001(hightemp), 3 pages, 2 figures, uses espcrc2.sty

We point out some problems with the previously-proposed phase diagram of the $Z_6$ spin models. Consideration of the diagram near to the decoupling surface using both exact and approximate arguments suggests a modification which remedies these deficiencies. With the aid of a new parametrisation of the phase space, we study the models numerically, with results which support our conjectures., Comment: 10 pages, Latex 2e, 4 figures, uses epsf, amssymb, cite

The one--loop determinant computed around the kink solution in the 3D $\phi^4$ theory, in cylindrical geometry, allows one to obtain the partition function of the interface separating coexisting phases. The quantum fluctuations of the interface around its equilibrium position are described by a $c=1$ two--dimensional conformal field theory, namely a 2D free massless scalar field living on the interface. In this way the capillary wave model conjecture for the interface free energy in its gaussian approximation is proved., Comment: latex, 9 pages, no figures

The physics of fluid interfaces between domains of different magnetization in the ordered phase of the 3D three-state Potts model is studied by means of a Monte Carlo simulation. It is shown that finite--size effects in the interface free energy are well described by the capillary wave model at two loop order, supporting the idea of the universality of this description of fluid interfaces in 3D statistical models., Comment: Latex file, 12 pages, 4 ps figures enclosed + 2 figures available on request

We consider the valley--method computation of the inclusive cross section of baryon number violating processes in the Standard Model. We show that any physically correct model of the valley action should present a singularity in the saddle point valley parameters as functions of the energy of the process. This singularity prevents the saddle point configuration from collapsing into the perturbative vacuum., Comment: 6 pages, LaTex, TPI-MINN-93/32-T

We consider the three--dimensional BF--model with planar boundary in the axial gauge. We find two--dimensional conserved chiral currents living on the boundary and satisfying Kac--Moody algebras., Comment: 18 pages