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Search Results: 1 - 10 of 6854 matches for " Thorsten Schmidt "
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Assignment of isochores for all completely sequenced vertebrate genomes using a consensus
Thorsten Schmidt, Dmitrij Frishman
Genome Biology , 2008, DOI: 10.1186/gb-2008-9-6-r104
Abstract: More than three decades ago gradient density analyses of fragmented DNA identified long compositionally homogenous regions on mammalian chromosomes, widely known as isochores [1-3] or long homogeneous genome regions [4], associated with a wide range of important biological properties. Gene density is up to 16 times higher in GC-rich isochores than in GC-poor isochores [5] (with GC referring to the percentage of the nucleotides guanine and cytosine), and the genes in the GC-rich isochores code for shorter proteins and are more compact with a smaller amount of introns [6]. It was also shown that the GC-rich codons, such as those coding for alanine and arginine, are more frequent in GC-rich isochores [7,8]. The distribution of repeat elements is influenced by the isochore structure of the genome: SINE (short-interspersed nuclear element) sequences tend to be more frequent in GC-rich isochores while the LINE (long-interspersed nuclear elements) sequences are preferentially found in GC-poorer regions [9-11]. The structure of chromosome bands also correlates with isochores: T-bands predominantly consist of GC-rich isochores, while the GC-poorer isochores are found in G-bands [12-14]. The recombination frequency is higher [15,16] and replication starts up to two hours earlier [17] in regions with high GC content.Further progress in understanding the biological role and evolution of long-range variation in base composition is seriously hindered by the lack of objective and generally accepted isochore assignment methods. A multitude of computational approaches has been developed by various groups [18-23], but no single resource allows the accession, comparison, and combination of isochore assignments made by various techniques in different genomes. Here we introduce a new consensus predictor that characterizes the level of support for isochore locations determined by individual methods. We present a database of isochore maps for all completely sequenced vertebrate genomes an
PROMPT: a protein mapping and comparison tool
Thorsten Schmidt, Dmitrij Frishman
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-331
Abstract: PROMPT is a comprehensive bioinformatics software environment which enables the user to compare arbitrary protein sequence sets, revealing statistically significant differences in their annotation features. It allows automatic retrieval and integration of data from a multitude of molecular biological databases as well as from a custom XML format. Similarity-based mapping of sequence IDs makes it possible to link experimental information obtained from different sources despite discrepancies in gene identifiers and minor sequence variation. PROMPT provides a full set of statistical procedures to address the following four use cases: i) comparison of the frequencies of categorical annotations between two sets, ii) enrichment of nominal features in one set with respect to another one, iii) comparison of numeric distributions, and iv) correlation of numeric variables. Analysis results can be visualized in the form of plots and spreadsheets and exported in various formats, including Microsoft Excel.PROMPT is a versatile, platform-independent, easily expandable, stand-alone application designed to be a practical workhorse in analysing and mining protein sequences and associated annotation. The availability of the Java Application Programming Interface and scripting capabilities on one hand, and the intuitive Graphical User Interface with context-sensitive help system on the other, make it equally accessible to professional bioinformaticians and biologically-oriented users. PROMPT is freely available for academic users from http://webclu.bio.wzw.tum.de/prompt/ webcite.Molecular bioinformatics was born as a science of comparing individual DNA and amino acid sequences with each other. Over the past three decades important biological insights have been obtained by establishing unexpected sequence similarity between seemingly unrelated proteins (e.g., Koonin et al. [1]). More recently, modern high-throughput technologies (genome sequencing, expression profiling, mass spectromet
Stabilit t von Bewertungen zur Auswahl von Systeml sungen am Beispiel automatisierter Kommissioniersysteme für Beutelware
Schmidt, Thorsten,Leiking, Lars
Logistics Journal : Referierte Ver?ffentlichungen , 2005,
Abstract: Der Druck auf Kosteneinsparungen und Produktivit tszuwachs in Bereichen der Kommissionierung und somit auch der Wunsch nach Rationalisierung durch Automatisierung wachsen stetig. Besonders bei in Beuteln verpackten Artikeln gestaltet sich jedoch eine Automatisierung der Kommissioniervorg nge aufgrund der mechanischen Produkteigenschaften schwierig. Entsprechende Systeme sind erst noch zu entwickeln. Im Systementwicklungsprozess m chte man m glichst frühzeitig Entscheidungen treffen k nnen, um die technisch-wirtschaftlich sinnvollste L sungsvariante auszuw hlen und Entwicklungsaufwand einzusparen. Dieser Artikel besch ftigt sich mit den Eigenschaften besagter Produkte im Hinblick auf deren automatisierte Handhabung und zeigt einen konstruktionsmethodischen Ansatz zur Bewertung systemtechnischer L sungsans tze mit zugeh rigerer Sensitivit tsanalyse auf.
Reliability of evaluations for the choice of system solutions at the example of automated order-picking systems for bagged goods
Schmidt, Thorsten,Leiking, Lars
Logistics Journal : Referierte Ver?ffentlichungen , 2005,
Abstract: There is a steadily increasing pressure on cost-savings and productivity growth in sectors of order-picking such that the wish for rationalization by automation is rising. Special problems are faced trying to automatize handling operations of order-picking articles packed in bags. The mechanical properties of the objects and their hard-to-predict shape and position represent obstacles and are complicating handling operations. A systematic approach in system design is required. This article deals with the properties of such products under aspects of difficulties arising in automated handling and points out a useful system development methodology.
A generalized intensity based framework for single-name credit risk
Frank Gehmlich,Thorsten Schmidt
Quantitative Finance , 2015,
Abstract: The intensity of a default time is obtained by assuming that the default indicator process has an absolutely continuous compensator. Here we drop the assumption of absolute continuity with respect to the Lebesgue measure and only assume that the compensator is absolutely continuous with respect to a general $\sigma$-finite measure. This allows for example to incorporate the Merton-model in the generalized intensity based framework. An extension of the Black-Cox model is also considered. We propose a class of generalized Merton models and study absence of arbitrage by a suitable modification of the forward rate approach of Heath-Jarrow-Morton (1992). Finally, we study affine term structure models which fit in this class. They exhibit stochastic discontinuities in contrast to the affine models previously studied in the literature.
Dynamic Defaultable Term Structure Modelling beyond the Intensity Paradigm
Frank Gehmlich,Thorsten Schmidt
Quantitative Finance , 2014,
Abstract: The two main approaches in credit risk are the structural approach pioneered in Merton (1974) and the reduced-form framework proposed in Jarrow & Turnbull (1995) and in Artzner & Delbaen (1995). The goal of this article is to provide a unified view on both approaches. This is achieved by studying reduced-form approaches under weak assumptions. In particular we do not assume the global existence of a default intensity and allow default at fixed or predictable times with positive probability, such as coupon payment dates. In this generalized framework we study dynamic term structures prone to default risk following the forward-rate approach proposed in Heath-Jarrow-Morton (1992). It turns out, that previously considered models lead to arbitrage possibilities when default may happen at a predictable time with positive probability. A suitable generalization of the forward-rate approach contains an additional stochastic integral with atoms at predictable times and necessary and sufficient conditions for a suitable no-arbitrage condition (NAFL) are given. In the view of efficient implementations we develop a new class of affine models which do not satisfy the standard assumption of stochastic continuity. The chosen approach is intimately related to the theory of enlargement of filtrations, to which we provide a small example by means of filtering theory where the Azema supermartingale contains upward and downward jumps, both at predictable and totally inaccessible stopping times.
Dynamic Term Structure Modelling with Default and Mortality Risk: New Results on Existence and Monotonicity
Stefan Tappe,Thorsten Schmidt
Quantitative Finance , 2013,
Abstract: This paper considers general term structure models like the ones appearing in portfolio credit risk modelling or life insurance. We give a general model starting from families of forward rates driven by infinitely many Brownian motions and an integer-valued random measure, generalizing existing approaches in the literature. Then we derive drift conditions which are equivalent to no asymptotic free lunch on the considered market. Existence results are also given. In practice, models possessing a certain monotonicity are favorable and we study general conditions which guarantee this. The setup is illustrated with some examples.
CDO term structure modelling with Levy processes and the relation to market models
Thorsten Schmidt,Jerzy Zabczyk
Quantitative Finance , 2010, DOI: 10.1142/S0219024911006462
Abstract: This paper considers the modelling of collateralized debt obligations (CDOs). We propose a top-down model via forward rates generalizing Filipovi\'c, Overbeck and Schmidt (2009) to the case where the forward rates are driven by a finite dimensional L\'evy process. The contribution of this work is twofold: we provide conditions for absence of arbitrage in this generalized framework. Furthermore, we study the relation to market models by embedding them in the forward rate framework in spirit of Brace, Gatarek and Musiela (1997).
On Galerkin Approximations for the Zakai Equation with Diffusive and Point Process Observations
Rüdiger Frey,Thorsten Schmidt,Ling Xu
Mathematics , 2013,
Abstract: This paper studies Galerkin approximations applied to the Zakai equation of stochastic filtering. The basic idea of this approach is to project the infinite-dimensional Zakai equation onto some finite-dimensional subspace generated by smooth basis functions; this leads to a finite-dimensional system of stochastic differential equations that can be solved numerically. The contribution of the paper is twofold. On the theoretical side, existing convergence results are extended to filtering models with observations of point-process or mixed type. On the applied side, various issues related to the numerical implementation of the method are considered; in particular, we propose to work with a subspace that is constructed from a basis of Hermite polynomials. The paper closes with a numerical case study.
When roll-overs do not qualify as numéraire: bond markets beyond short rate paradigms
Irene Klein,Thorsten Schmidt,Josef Teichmann
Quantitative Finance , 2013,
Abstract: We investigate default-free bond markets where the standard relationship between a possibly existing bank account process and the term structure of bond prices is broken, i.e. the bank account process is not a valid num\'eraire. We argue that this feature is not the exception but rather the rule in bond markets when starting with, e.g., terminal bonds as num\'eraires. Our setting are general c\`adl\`ag processes as bond prices, where we employ directly methods from large financial markets. Moreover, we do not restrict price process to be semimartingales, which allows for example to consider markets driven by fractional Brownian motion. In the core of the article we relate the appropriate no arbitrage assumptions (NAFL), i.e. no asymptotic free lunch, to the existence of an equivalent local martingale measure with respect to the terminal bond as num\'eraire, and no arbitrage opportunities of the first kind (NAA1) to the existence of a supermartingale deflator, respectively. In all settings we obtain existence of a generalized bank account as a limit of convex combinations of roll-over bonds. Additionally we provide an alternative definition of the concept of a num\'eraire, leading to a possibly interesting connection to bubbles. If we can construct a bank account process through roll-overs, we can relate the impossibility of taking the bank account as num\'eraire to liquidity effects. Here we enter endogenously the arena of multiple yield curves. The theory is illustrated by several examples.
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