CORG: a database for COmparative Regulatory Genomics

Sequence conservation in non-coding, upstream regions of orthologous genes from man and mouse is likely to reflect common regulatory DNA sites. Motivated by this assumption we have delineated a catalogue of conserved non-coding sequence blocks and provide the CORG-'COmparative Regulatory Genomics'-database. The data were computed based on statistically significant local suboptimal alignments of 15 kb regions upstream of the translation start sites of, currently, 10 793 pairs of orthologous genes. The resulting conserved non-coding blocks were annotated with EST matches for easier detection of non-coding mRNA and with hits to known transcription factor binding sites. CORG data are accessible from the ENSEMBL web site via a DAS service as well as a specially developed web service (http://corg.molgen.mpg.de) for query and interactive visualization of the conserved blocks and their annotation

Rotor interaction in the annulus billiard

Introducing the rotor interaction in the integrable system of the annulus billiard produces a variety of dynamical phenomena, from integrability to ergodicity

Lyapunov instability for a periodic Lorentz gas thermostated by deterministic scattering

In recent work a deterministic and time-reversible boundary thermostat called thermostating by deterministic scattering has been introduced for the periodic Lorentz gas [Phys. Rev. Lett. {\bf 84}, 4268 (2000)]. Here we assess the nonlinear properties of this new dynamical system by numerically calculating its Lyapunov exponents. Based on a revised method for computing Lyapunov exponents, which employs periodic orthonormalization with a constraint, we present results for the Lyapunov exponents and related quantities in equilibrium and nonequilibrium. Finally, we check whether we obtain the same relations between quantities characterizing the microscopic chaotic dynamics and quantities characterizing macroscopic transport as obtained for conventional deterministic and time-reversible bulk thermostats.Comment: 18 pages (revtex), 7 figures (postscript

Systems biologists seek fuller integration of systems biology approaches in new cancer research programs

Systems biology takes an interdisciplinary approach to the systematic study of complex interactions in biological systems. This approach seeks to decipher the emergent behaviors of complex systems rather than focusing only on their constituent properties. As an increasing number of examples illustrate the value of systems biology approaches to understand the initiation, progression, and treatment of cancer, systems biologists from across Europe and the United States hope for changes in the way their field is currently perceived among cancer researchers. In a recent EU-US workshop, supported by the European Commission, the German Federal Ministry for Education and Research, and the National Cancer Institute of the NIH, the participants discussed the strengths, weaknesses, hurdles, and opportunities in cancer systems biology

Determining significance of pairwise co-occurrences of events in bursty sequences

<p>Abstract</p> <p>Background</p> <p>Event sequences where different types of events often occur close together arise, e.g., when studying potential transcription factor binding sites (TFBS, events) of certain transcription factors (TF, types) in a DNA sequence. These events tend to occur in bursts: in some genomic regions there are more genes and therefore potentially more binding sites, while in some, possibly very long regions, hardly any events occur. Also some types of events may occur in the sequence more often than others.</p> <p>Tendencies of co-occurrence of binding sites of two or more TFs are interesting, as they may imply a co-operative role between the TFs in regulatory processes. Determining a numerical value to summarize the tendency for co-occurrence between two TFs can be done in a number of ways. However, testing for the significance of such values should be done with respect to a relevant null model that takes into account the global sequence structure.</p> <p>Results</p> <p>We extend the existing techniques that have been considered for determining the significance of co-occurrence patterns between a pair of event types under different null models. These models range from very simple ones to more complex models that take the burstiness of sequences into account. We evaluate the models and techniques on synthetic event sequences, and on real data consisting of potential transcription factor binding sites.</p> <p>Conclusion</p> <p>We show that simple null models are poorly suited for bursty data, and they yield many false positives. More sophisticated models give better results in our experiments. We also demonstrate the effect of the window size, i.e., maximum co-occurrence distance, on the significance results.</p

ThermoElectric Transport Properties of a Chain of Quantum Dots with Self-Consistent Reservoirs

We introduce a model for charge and heat transport based on the Landauer-Buttiker scattering approach. The system consists of a chain of $N$ quantum dots, each of them being coupled to a particle reservoir. Additionally, the left and right ends of the chain are coupled to two particle reservoirs. All these reservoirs are independent and can be described by any of the standard physical distributions: Maxwell-Boltzmann, Fermi-Dirac and Bose-Einstein. In the linear response regime, and under some assumptions, we first describe the general transport properties of the system. Then we impose the self-consistency condition, i.e. we fix the boundary values (T_L,\mu_L) and (T_R,mu_R), and adjust the parameters (T_i,mu_i), for i = 1,...,N, so that the net average electric and heat currents into all the intermediate reservoirs vanish. This condition leads to expressions for the temperature and chemical potential profiles along the system, which turn out to be independent of the distribution describing the reservoirs. We also determine the average electric and heat currents flowing through the system and present some numerical results, using random matrix theory, showing that these currents are typically governed by Ohm and Fourier laws.Comment: Minor changes (45 pages

Coherent States Measurement Entropy

Coherent states (CS) quantum entropy can be split into two components. The dynamical entropy is linked with the dynamical properties of a quantum system. The measurement entropy, which tends to zero in the semiclassical limit, describes the unpredictability induced by the process of a quantum approximate measurement. We study the CS--measurement entropy for spin coherent states defined on the sphere discussing different methods dealing with the time limit $n \to \infty$. In particular we propose an effective technique of computing the entropy by iterated function systems. The dependence of CS--measurement entropy on the character of the partition of the phase space is analysed.Comment: revtex, 22 pages, 14 figures available upon request (e-mail: [email protected]). Submitted to J.Phys.

On the Fluctuation Relation for Nose-Hoover Boundary Thermostated Systems

We discuss the transient and steady state fluctuation relation for a mechanical system in contact with two deterministic thermostats at different temperatures. The system is a modified Lorentz gas in which the fixed scatterers exchange energy with the gas of particles, and the thermostats are modelled by two Nos\'e-Hoover thermostats applied at the boundaries of the system. The transient fluctuation relation, which holds only for a precise choice of the initial ensemble, is verified at all times, as expected. Times longer than the mesoscopic scale, needed for local equilibrium to be settled, are required if a different initial ensemble is considered. This shows how the transient fluctuation relation asymptotically leads to the steady state relation when, as explicitly checked in our systems, the condition found in [D.J. Searles, {\em et al.}, J. Stat. Phys. 128, 1337 (2007)], for the validity of the steady state fluctuation relation, is verified. For the steady state fluctuations of the phase space contraction rate \zL and of the dissipation function \zW, a similar relaxation regime at shorter averaging times is found. The quantity \zW satisfies with good accuracy the fluctuation relation for times larger than the mesoscopic time scale; the quantity \zL appears to begin a monotonic convergence after such times. This is consistent with the fact that \zW and \zL differ by a total time derivative, and that the tails of the probability distribution function of \zL are Gaussian.Comment: Major revision. Fig.10 was added. Version to appear in Journal of Statistical Physic

Nucleic Acids Res.

Sequence conservation in non-coding, upstream regions of orthologous genes from man and mouse is likely to reflect common regulatory DNA sites. Motivated by this assumption we have delineated a catalogue of conserved non-coding sequence blocks and provide the CORG—‘COmparative Regulatory Genomics’—database. The data were computed based on statistically significant local suboptimal alignments of 15 kb regions upstream of the translation start sites of, currently, 10 793 pairs of orthologous genes. The resulting conserved non-coding blocks were annotated with EST matches for easier detection of non-coding mRNA and with hits to known transcription factor binding sites. CORG data are accessible from the ENSEMBL web site via a DAS service as well as a specially developed web service (http://corg.molgen.mpg.de) for query and interactive visualization of the conserved blocks and their annotation