Search results for "bioinformatics"
showing 10 items of 1632 documents
kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers.
2018
Abstract Motivation K-mers along with their frequency have served as an elementary building block for error correction, repeat detection, multiple sequence alignment, genome assembly, etc., attracting intensive studies in k-mer counting. However, the output of k-mer counters itself is large; very often, it is too large to fit into main memory, leading to highly narrowed usability. Results We introduce a novel idea of encoding k-mers as well as their frequency, achieving good memory saving and retrieval efficiency. Specifically, we propose a Bloom filter-like data structure to encode counted k-mers by coupled-bit arrays—one for k-mer representation and the other for frequency encoding. Exper…
Misinterpretation risks of global stochastic optimisation of kinetic models revealed by multiple optimisation runs
2016
Abstract One of use cases for metabolic network optimisation of biotechnologically applied microorganisms is the in silico design of new strains with an improved distribution of metabolic fluxes. Global stochastic optimisation methods (genetic algorithms, evolutionary programing, particle swarm and others) can optimise complicated nonlinear kinetic models and are friendly for unexperienced user: they can return optimisation results with default method settings (population size, number of generations and others) and without adaptation of the model. Drawbacks of these methods (stochastic behaviour, undefined duration of optimisation, possible stagnation and no guaranty of reaching optima) cau…
Crystal structure of ethyl 2-(di-eth-oxy-phosphor-yl)-2-(2,3,4-tri-meth-oxy-phen-yl)acetate.
2014
The title compound, C17H27O8P, was prepared by Michaelis–Arbuzov reaction of ethyl 2-bromo-2-(2,3,4-trimethoxyphenyl)acetate and triethyl phosphite. Such compounds rarely crystallize, but single crystals were recovered after the initial oil was left for approximately 10 years. The bond angle of thesp3-hybridized C atom connecting the benzene derivative with the phospho unit is widened marginally [112.5 (2)°]. The terminal P—O bond length of 1.464 (2) Å clearly indicates a double bond, whereas the two O atoms of the ethoxy groups connected to the phosphorous atom have bond lengths of 1.580 (2) Å and 1.581 (3) Å. The three methoxy groups emerge out of the benzene-ring plane due to steric hind…
Complex Detection in Protein-Protein Interaction Networks: A Compact Overview for Researchers and Practitioners
2012
The availability of large volumes of protein-protein interaction data has allowed the study of biological networks to unveil the complex structure and organization in the cell. It has been recognized by biologists that proteins interacting with each other often participate in the same biological processes, and that protein modules may be often associated with specific biological functions. Thus the detection of protein complexes is an important research problem in systems biology. In this review, recent graph-based approaches to clustering protein interaction networks are described and classified with respect to common peculiarities. The goal is that of providing a useful guide and referenc…
Comparison of Prognostic Signatures in Node-Negative Tamoxifen-Treated Breast Cancer Patients.
2009
Abstract Background: A number of molecular signatures have been published to aid breast cancer prognosis and therapy response prediction. A 76-gene signature has been developed in a node-negative patient cohort that did not receive systemic therapy.1 Another prognostic 97-gene signature measures predominantly proliferation-associated genes.2 Finally, a 21-gene signature has been developed for node-negative and estrogen receptor–positive breast cancer patients treated with tamoxifen in the adjuvant setting.3 Here we compare the prognostic performance of all three published algorithms in a cohort of 189 node-negative breast cancer patients treated with tamoxifen.Materials and Methods: Fresh-f…
2-Methyl-4-phenyl-3,4-dihydroquinazoline
2011
The title compound, C15H14N2, was formed during the lithiation of 2-methylquinazoline with phenyllithium followed by hydrolysis of the intermediate lithium 2-methyl-4-phenyl-4H-quinazolin-3-ide. NMR spectra as well as single-crystal X-ray structural data indicate that the reaction product to have the same structure in chloroform solution as in the crystalline state. The phenyl substituent is twisted out of the plane of the 3,4-dihydroquinazoline ring system by 86.47 (7)°. In the crystal, intermolecular N—H...N interactions connect the molecules into infinite chains.
Crystal structure ofp-toluenesulfonylmethyl isocyanide
2015
The molecule of the commercially available title compound, C9H9NO2S, has crystallographically imposed mirror symmetry, the mirror plane passing through the isocyanide group and thepara-C atoms, the methyl C atom and the S atom of the methyl 4-tolyl sulfone moiety. In the crystal, C—H...O hydrogen-bond interactions link the molecules into chains running parallel to thebaxis.
Strong vacuum squeezing from bichromatically driven Kerrlike cavities: from optomechanics to superconducting circuits
2015
AbstractSqueezed light, displaying less fluctuation than vacuum in some observable, is key in the flourishing field of quantum technologies. Optical or microwave cavities containing a Kerr nonlinearity are known to potentially yield large levels of squeezing, which have been recently observed in optomechanics and nonlinear superconducting circuit platforms. Such Kerr-cavity squeezing however suffers from two fundamental drawbacks. First, optimal squeezing requires working close to turning points of a bistable cycle, which are highly unstable against noise thus rendering optimal squeezing inaccessible. Second, the light field has a macroscopic coherent component corresponding to the pump, ma…
Differenzierte chirurgische Therapie neuroendokriner Tumoren (NET) des Magens
2010
Neuroendocrine tumours (NET) of the stomach have increasingly entered into the focus of attention recently by endocrinologists as well as by surgeons on account of new findings on their biological background and their clinical relevance. The discriminating pathogenesis and the basically different biological behaviours of neuroendocrine tumours of the stomach require a differentiated therapeutical treatment for the different sub-types. The differential diagnostic clarification of the basic pathomechanism is therefore of decisive importance. As a consequence of the rarity of this entity, any treatment should be performed in corresponding centres. An interdisciplinary therapy planning, e. g., …
Designing de novo: interdisciplinary debates in synthetic biology
2013
Synthetic biology is often presented as a promissory field that ambitions to produce novelty by design. The ultimate promise is the production of living systems that will perform new and desired functions in predictable ways. Nevertheless, realizing promises of novelty has not proven to be a straightforward endeavour. This paper provides an overview of, and explores the existing debates on, the possibility of designing living systems de novo as they appear in interdisciplinary talks between engineering and biological views within the field of synthetic biology. To broaden such interdisciplinary debates, we include the views from the social sciences and the humanities and we point to some fu…