The Next Great Exoplanet Hunt

What strange new worlds will our next-generation telescopes find?Comment: Published in American Scientist: Volume 103, Number 3, Pages 196 to 203 (http://www.americanscientist.org/issues/feature/2015/3/the-next-great-exoplanet-hunt). Error concerning liquid helium correcte

The Next Generation Transit Survey—Prototyping Phase

We present the prototype telescope for the Next Generation Transit Survey, which was built in the UK in 2008/2009 and tested on La Palma in the Canary Islands in 2010. The goals for the prototype system were severalfold: to determine the level of systematic noise in an NGTS-like system; demonstrate that we can perform photometry at the (sub) millimagnitude level on transit timescales across a wide-field; show that it is possible to detect transiting super-Earth and Neptune-sized exoplanets and prove the technical feasibility of the proposed planet survey. We tested the system for around 100 nights and met each of the goals above. Several key areas for improvement were highlighted during the prototyping phase. They have been subsequently addressed in the final NGTS facility, which was recently commissioned at ESO Cerro Paranal, Chile

Change-point model on nonhomogeneous Poisson processes with application in copy number profiling by next-generation DNA sequencing

We propose a flexible change-point model for inhomogeneous Poisson Processes, which arise naturally from next-generation DNA sequencing, and derive score and generalized likelihood statistics for shifts in intensity functions. We construct a modified Bayesian information criterion (mBIC) to guide model selection, and point-wise approximate Bayesian confidence intervals for assessing the confidence in the segmentation. The model is applied to DNA Copy Number profiling with sequencing data and evaluated on simulated spike-in and real data sets.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS517 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Next-generation sequencing: applications beyond genomes.

The development of DNA sequencing more than 30 years ago has profoundly impacted biological research. In the last couple of years, remarkable technological innovations have emerged that allow the direct and cost-effective sequencing of complex samples at unprecedented scale and speed. These next-generation technologies make it feasible to sequence not only static genomes, but also entire transcriptomes expressed under different conditions. These and other powerful applications of next-generation sequencing are rapidly revolutionizing the way genomic studies are carried out. Below, we provide a snapshot of these exciting new approaches to understanding the properties and functions of genomes. Given that sequencing-based assays may increasingly supersede microarray-based assays, we also compare and contrast data obtained from these distinct approaches

The Effect of Network and Infrastructural Variables on SPDY's Performance

HTTP is a successful Internet technology on top of which a lot of the web resides. However, limitations with its current specification, i.e. HTTP/1.1, have encouraged some to look for the next generation of HTTP. In SPDY, Google has come up with such a proposal that has growing community acceptance, especially after being adopted by the IETF HTTPbis-WG as the basis for HTTP/2.0. SPDY has the potential to greatly improve web experience with little deployment overhead. However, we still lack an understanding of its true potential in different environments. This paper seeks to resolve these issues, offering a comprehensive evaluation of SPDY's performance using extensive experiments. We identify the impact of network characteristics and website infrastructure on SPDY's potential page loading benefits, finding that these factors are decisive for SPDY and its optimal deployment strategy. Through this, we feed into the wider debate regarding HTTP/2.0, exploring the key aspects that impact the performance of this future protocol

Linking de novo assembly results with long DNA reads by dnaasm-link application

Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from next-generation and third-generation sequencing. Herein, we present a new application called dnaasm-link for linking contigs, a result of \textit{de novo} assembly of second-generation sequencing data, with long DNA reads. Our tool includes an integrated module to fill gaps with a suitable fragment of appropriate long DNA read, which improves the consistency of the resulting DNA sequences. This feature is very important, in particular for complex DNA regions, as presented in the paper. Finally, our implementation outperforms other state-of-the-art tools in terms of speed and memory requirements, which may enable the usage of the presented application for organisms with a large genome, which is not possible in~existing applications. The presented application has many advantages as (i) significant memory optimization and reduction of computation time (ii) filling the gaps through the appropriate fragment of a specified long DNA read (iii) reducing number of spanned and unspanned gaps in the existing genome drafts. The application is freely available to all users under GNU Library or Lesser General Public License version 3.0 (LGPLv3). The demo application, docker image and source code are available at http://dnaasm.sourceforge.net.Comment: 16 pages, 5 figure

Limit theorems for bifurcating Markov chains. Application to the detection of cellular aging

We propose a general method to study dependent data in a binary tree, where an individual in one generation gives rise to two different offspring, one of type 0 and one of type 1, in the next generation. For any specific characteristic of these individuals, we assume that the characteristic is stochastic and depends on its ancestors' only through the mother's characteristic. The dependency structure may be described by a transition probability $P(x,dy dz)$ which gives the probability that the pair of daughters' characteristics is around $(y,z)$, given that the mother's characteristic is $x$. Note that $y$, the characteristic of the daughter of type 0, and $z$, that of the daughter of type 1, may be conditionally dependent given $x$, and their respective conditional distributions may differ. We then speak of bifurcating Markov chains. We derive laws of large numbers and central limit theorems for such stochastic processes. We then apply these results to detect cellular aging in Escherichia Coli, using the data of Stewart et al. and a bifurcating autoregressive model.Comment: Published in at http://dx.doi.org/10.1214/105051607000000195 the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org