| 1. |
- Aurell, Erik, 1961-, et al.
(författare)
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The bulk and the tail of minimal absent words in genome sequences
- 2016
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Ingår i: Physical Biology. - : Institute of Physics (IOP). - 1478-3967 .- 1478-3975. ; 13:2
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Tidskriftsartikel (refereegranskat)abstract
- Minimal absent words (MAW) of a genomic sequence are subsequences that are absent themselves but the subwords of which are all present in the sequence. The characteristic distribution of genomic MAWs as a function of their length has been observed to be qualitatively similar for all living organisms, the bulk being rather short, and only relatively few being long. It has been an open issue whether the reason behind this phenomenon is statistical or reflects a biological mechanism, and what biological information is contained in absent words. % In this work we demonstrate that the bulk can be described by a probabilistic model of sampling words from random sequences, while the tail of long MAWs is of biological origin. We introduce the novel concept of a core of a minimal absent word, which are sequences present in the genome and closest to a given MAW. We show that in bacteria and yeast the cores of the longest MAWs, which exist in two or more copies, are located in highly conserved regions the most prominent example being ribosomal RNAs (rRNAs). We also show that while the distribution of the cores of long MAWs is roughly uniform over these genomes on a coarse-grained level, on a more detailed level it is strongly enhanced in 3' untranslated regions (UTRs) and, to a lesser extent, also in 5' UTRs. This indicates that MAWs and associated MAW cores correspond to fine-tuned evolutionary relationships, and suggest that they can be more widely used as markers for genomic complexity.
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| 2. |
- Bogdanowicz, Janusz, et al.
(författare)
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Light absorption in conical silicon particles
- 2013
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Ingår i: Optics Express. - 1094-4087. ; 21:3, s. 3891-3896
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Tidskriftsartikel (refereegranskat)abstract
- The problem of the absorption of light by a nanoscale dielectric cone is discussed. A simplified solution based on the analytical Mie theory of scattering and absorption by cylindrical objects is proposed and supported by the experimental observation of sharply localized holes in conical silicon tips after high-fluence irradiation. This study reveals that light couples with tapered objects dominantly at specific locations, where the local radius corresponds to one of the resonant radii of a cylindrical object, as predicted by Mie theory.
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| 3. |
- Chatterjee, Saikat, et al.
(författare)
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SEK: Sparsity exploiting k-mer-based estimation of bacterial community composition
- 2014
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Ingår i: Bioinformatics. - : Oxford University Press. - 1460-2059 .- 1367-4803 .- 1367-4811. ; 30:17, s. 2423-2431
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: Estimation of bacterial community composition from a high-throughput sequenced sample is an important task in metagenomics applications. As the sample sequence data typically harbors reads of variable lengths and different levels of biological and technical noise, accurate statistical analysis of such data is challenging. Currently popular estimation methods are typically time-consuming in a desktop computing environment.Results: Using sparsity enforcing methods from the general sparse signal processing field (such as compressed sensing), we derive a solution to the community composition estimation problem by a simultaneous assignment of all sample reads to a pre-processed reference database. A general statistical model based on kernel density estimation techniques is introduced for the assignment task, and the model solution is obtained using convex optimization tools. Further, we design a greedy algorithm solution for a fast solution. Our approach offers a reasonably fast community composition estimation method, which is shown to be more robust to input data variation than a recently introduced related method.Availability and implementation: A platform-independent Matlab implementation of the method is freely available at http://www.ee.kth.se/ctsoftware; source code that does not require access to Matlab is currently being tested and will be made available later through the above Web site.
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| 4. |
- Innocenti, Nicolas, 1986-, et al.
(författare)
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An observation of circular RNAs in bacterial RNA-seq data.
- 2015
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Circular RNAs (circRNAs) are a class of RNA with an important role in micro RNA (miRNA) regulation recently discovered in Human and various other eukaryotes as well as in archaea. Here, we have analyzed RNA-seq data obtained from Enterococcus faecalis and Escherichia coli in a way similar to previous studies performed on eukaryotes. We report observations of circRNAs in RNA-seq data that are reproducible across multiple experiments performed with different protocols or growth conditions.
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| 5. |
- Innocenti, Nicolas, 1986-
(författare)
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Data Analysis and Next Generation Sequencing : Applications in Microbiology.
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Next Generation Sequencing (NGS) is a new technology that has revolutionized the way we study living organisms. Where previously only a few genes could be studied at a time through targeted direct probing, NGS offers the possibility to perform measurements for a whole genome at once. The drawback is that the amount of data generated in the process is large and extracting useful information from it requires new methods to process and analyze it.The main contribution of this thesis is the development of a novel experimental method coined tagRNA-seq, combining 5’tagRACE, a previously developed technique, with RNA-sequencing technology. Briefly, tagRNA-seq makes it possible to identify the 5’ ends of RNAs in bacteria and directly probe for their type, primary or processed, by ligating short RNA sequences, the tags, to the beginnings of RNA molecules. We used the method to directly probe for transcription start and processing sites in two bacterial species, Escherichiacoli and Enterococcus faecalis. It was also used to study polyadenylation in E. coli, where the ability to identify processed RNA molecules proved to be useful to separate direct and indirect regulatory effects of this mechanism. We also demonstrate how data from tagRNA-seq experiments can be used to increase confidence on the discovery of anti-sense transcripts in bacteria. Analyses of RNA-seq data obtained in the context of these experiments revealed subtle artifacts in the coverage signal towards gene ends, that we were able to explain and quantify based Kolmogorov’s broken stick model. We also discovered evidences for circularization of a few RNA transcripts, both in our own data sets and publicly available data.Designing the tags used in tagRNA-seq led us to the problem of words absent from a text. We focus on a particular subset of these, the minimal absent words (MAWs), and develop a theory providing a complete description of their size distribution in random text. We also show that MAWs in genomes from viruses and living organisms almost always exhibit a behavior different from random texts in the tail of the distribution, and that MAWs from this tail are closely related to sequences present in the genome that preferentially appear in regions with important regulatory functions.Finally, and independently from tagRNA-seq, we propose a new approach to the problem of bacterial community reconstruction in metagenomic, based on techniques from compressed sensing. We provide a novel algorithm competing with state-of-the-art techniques in the field.
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| 6. |
- Innocenti, Nicolas, 1986-, et al.
(författare)
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Detection and quantitative estimation of spurious double stranded DNA formation during reverse transcription in bateria using tagRNA-seq
- 2015
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Ingår i: RNA Biology. - : Taylor & Francis. - 1547-6286 .- 1555-8584.
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Tidskriftsartikel (refereegranskat)abstract
- Standard RNA-seq has a well know tendency to generate "ghost" antisense reads due to formation of spurious second strand cDNA in the sequencing process. We recently reported on a novel variant of RNA-seq coined "tagRNA-seq" introduced for the purpose of distinguishing primary from processed transcripts in bacteria. Incidentally, the additional information provided by the tag is also very suitable for detection of true anti-sense RNA transcripts and quantification of spurious antisense signals in a sample. We briefly explain how to perform such a detection and illustrate on previously published datasets.
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| 7. |
- Innocenti, Nicolas, 1986-, et al.
(författare)
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External field enhancement in coupled polymer microcavities - New options for integrated photonic components
- 2009
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Ingår i: European Conference on Lasers and Electro-Optics 2009 and the European Quantum Electronics Conference. CLEO Europe - EQEC 2009. - 9781424440795
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Microcavities are key components for integrated optical devices and systems. In this paper, enhancement of the resonance electric field outside a pair of coupled polymeric microcavities of hexagonal shape is investigated. Using numerical simulation, enhancement of outside-cavity field has been demonstrated in different sections of the coupled cavity system depending on particular design. Resonance frequencies are in visible part of electromagnetic spectrum. In reported simulations rigorous models based on solving Maxwell equations for propagating electromagnetic field in polymeric materials commonly used in nano-imprinting lithography is demonstrated.
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| 8. |
- Innocenti, Nicolas, 1986-, et al.
(författare)
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Lognormality and oscillations in the coverage of high-throughput transcriptomic data towards gene ends
- 2013
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Ingår i: Journal of Statistical Mechanics. - : Institute of Physics (IOP). - 1742-5468 .- 1742-5468. ; 2013:10, s. P10013-
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Tidskriftsartikel (refereegranskat)abstract
- High-throughput transcriptomics experiments have reached the stage where the count of the number of reads alignable to a given position can be treated as an almost-continuous signal. This allows us to ask questions of biophysical/biotechnical nature, but which may still have biological implications. Here we show that when sequencing RNA fragments from one end, as is the case on most platforms, an oscillation in the read count is observed at the other end. We further show that these oscillations can be well described by Kolmogorov's 1941 broken stick model. We investigate how the model can be used to improve predictions of gene ends (3' transcript ends), but conclude that with present data the improvement is only marginal. The results highlight subtle effects in high-throughput transcriptomics experiments which do not have a biological origin, but which may still be used to obtain biological information.
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| 9. |
- Innocenti, Nicolas, 1986-, et al.
(författare)
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Whole-genome mapping of 5′ RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis
- 2015
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Ingår i: RNA. - : RNA Society. - 1355-8382 .- 1469-9001.
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Tidskriftsartikel (refereegranskat)abstract
- Enterococcus faecalis is the third cause of nosocomial infections. To obtain the first snapshot of transcriptional organizations in this bacterium, we used a modified RNA-seq approach enabling to discriminate primary from processed 5' RNA ends. We also validated our approach by confirming known features in Escherichia coli. We mapped 559 transcription start sites (TSSs) and 352 processing sites (PSSs) in E. faecalis. A blind motif search retrieved canonical features of SigA-and SigN-dependent promoters preceding transcription start sites mapped. We discovered 85 novel putative regulatory RNAs, small-and antisense RNAs, and 72 transcriptional antisense organizations. Presented data constitute a significant insight into bacterial RNA landscapes and a step toward the inference of regulatory processes at transcriptional and post-transcriptional levels in a comprehensive manner.
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| 10. |
- Koelling, Sebastian, et al.
(författare)
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Characteristics of cross-sectional atom probe analysis on semiconductor structures
- 2011
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Ingår i: Ultramicroscopy. - : Elsevier BV. - 0304-3991 .- 1879-2723. ; 111:6, s. 540-545
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Tidskriftsartikel (refereegranskat)abstract
- The laser-assisted Atom Probe has been proposed as a metrology tool for next generation semiconductor technologies requiring sub-nm spatial resolution. In order to assess its potential for the analysis of three-dimensional semiconductor structures like FinFETs, we have studied the Atom Probes lateral resolution on a silicon, silicon–germanium multilayer structure. We find that the interactions of the laser with the semiconductor materials in the sample distort the sample surface. This results in transient errors of the measured dimensions of the structure. The deformation of the sample furthermore leads to a degradation of the lateral resolution. In the experiments presented in this paper, the Atom Probe reaches a lateral resolution of 1-1.8 nm/decade. In this paper we will discuss the reasons for the distortions of the tip and demonstrate that with the present state of data reconstruction severe quantification errors limit its applicability for the quantitative analysis of heterogeneous semiconductor structures. Our experiments show that reconstruction algorithms taking into account the time dependent nanostructure of the tip shape are required to arrive at accurate results.
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