Efficient Computation of Sequence Mappability

Sequence mappability is an important task in genome re-sequencing. In the $(k,m)$-mappability problem, for a given sequence $T$ of length $n$, our goal is to compute a table whose $i$th entry is the number of indices $j \ne i$ such that length-$m$ substrings of $T$ starting at positions $i$ and $j$ have at most $k$ mismatches. Previous works on this problem focused on heuristic approaches to compute a rough approximation of the result or on the case of $k=1$. We present several efficient algorithms for the general case of the problem. Our main result is an algorithm that works in $\mathcal{O}(n \min\{m^k,\log^{k+1} n\})$ time and $\mathcal{O}(n)$ space for $k=\mathcal{O}(1)$. It requires a carefu l adaptation of the technique of Cole et al.~[STOC 2004] to avoid multiple counting of pairs of substrings. We also show $\mathcal{O}(n^2)$-time algorithms to compute all results for a fixed $m$ and all $k=0,\ldots,m$ or a fixed $k$ and all $m=k,\ldots,n-1$. Finally we show that the $(k,m)$-mappability problem cannot be solved in strongly subquadratic time for $k,m = \Theta(\log n)$ unless the Strong Exponential Time Hypothesis fails.Comment: Accepted to SPIRE 201

Reverse-Safe Data Structures for Text Indexing

We introduce the notion of reverse-safe data structures. These are data structures that prevent the reconstruction of the data they encode (i.e., they cannot be easily reversed). A data structure D is called z-reverse-safe when there exist at least z datasets with the same set of answers as the ones stored by D. The main challenge is to ensure that D stores as many answers to useful queries as possible, is constructed efficiently, and has size close to the size of the original dataset it encodes. Given a text of length n and an integer z, we propose an algorithm which constructs a z-reverse-safe data structure that has size O(n) and answers pattern matching queries of length at most d optimally, where d is maximal for any such z-reverse-safe data structure. The construction algorithm takes O(n ω log d) time, where ω is the matrix multiplication exponent. We show that, despite the n ω factor, our engineered implementation takes only a few minutes to finish for million-letter texts. We further show that plugging our method in data analysis applications gives insignificant or no data utility loss. Finally, we show how our technique can be extended to support applications under a realistic adversary model

Direct laser printing of thin-film polyaniline devices

We report the fabrication of electrically functional polyaniline thin-film microdevices. Polyaniline films were printed in the solid phase by Laser Induced Forward Transfer directly between Au electrodes on a Si/SiO2 substrate. To apply solid-phase deposition, aniline was in situ polymerized on quartz substrates. Laser deposition preserves the morphology of the films and delivers sharp features with controllable dimensions. The electrical characteristics of printed polyaniline present ohmic behavior, allowing for electroactive applications. Results on gas sensing of ammonia are presented.Comment: In Pres

Cooperative motion and growing length scales in supercooled confined liquids

Using molecular dynamics simulations we investigate the relaxation dynamics of a supercooled liquid close to a rough as well as close to a smooth wall. For the former situation the relaxation times increase strongly with decreasing distance from the wall whereas in the second case they strongly decrease. We use this dependence to extract various dynamical length scales and show that they grow with decreasing temperature. By calculating the frequency dependent average susceptibility of such confined systems we show that the experimental interpretation of such data is very difficult.Comment: 7 pages of Latex, 3 figure

Mode Coupling relaxation scenario in a confined glass former

Molecular dynamics simulations of a Lennard-Jones binary mixture confined in a disordered array of soft spheres are presented. The single particle dynamical behavior of the glass former is examined upon supercooling. Predictions of mode coupling theory are satisfied by the confined liquid. Estimates of the crossover temperature are obtained by power law fit to the diffusion coefficients and relaxation times of the late $\alpha$ region. The $b$ exponent of the von Schweidler law is also evaluated. Similarly to the bulk, different values of the exponent $\gamma$ are extracted from the power law fit to the diffusion coefficients and relaxation times.Comment: 5 pages, 4 figures, changes in the text, accepted for publication on Europhysics Letter

Transcriptome map of mouse isochores

Background: The availability of fully sequenced genomes and the implementation of transcriptome technologies have increased the studies investigating the expression profiles for a variety of tissues, conditions, and species. In this study, using RNA-seq data for three distinct tissues (brain, liver, and muscle), we investigate how base composition affects mammalian gene expression, an issue of prime practical and evolutionary interest.Results: We present the transcriptome map of the mouse isochores (DNA segments with a fairly homogeneous base composition) for the three different tissues and the effects of isochores' base composition on their expression activity. Our analyses also cover the relations between the genes' expression activity and their localization in the isochore families.Conclusions: This study is the first where next-generation sequencing data are used to associate the effects of both genomic and genic compositional properties to their corresponding expression activity. Our findings confirm previous results, and further support the existence of a relationship between isochores and gene expression. This relationship corroborates that isochores are primarily a product of evolutionary adaptation rather than a simple by-product of neutral evolutionary processes.</p