arXiv subjects

Claude Pasquier

Publications and source records attributed to Claude Pasquier.

14 recordsLinked to original sources

arXiv2016

Prediction of miRNA-disease associations with a vector space model

MicroRNAs play critical roles in many physiological processes. Their dysregulations are also closely related to the development and progression of various human diseases, including cancer. Therefore, identifying new microRNAs that are associated with diseases contributes to a better understanding of pathogenicity mechanisms. MicroRNAs also represent a tremendous opportunity in biotechnology for early diagnosis. To date, several in silico methods have been developed to address the issue of microRNA-disease association prediction. However, these methods have various limitations. In this study, we investigate the hypothesis that information attached to miRNAs and diseases can be revealed by distributional semantics. Our basic approach is to represent distributional information on miRNAs and diseases in a high-dimensional vector space and to define associations between miRNAs and diseases in terms of their vector similarity. Cross validations performed on a dataset of known miRNA-disease associations demonstrate the excellent performance of our method. Moreover, the case study focused on breast cancer confirms the ability of our method to discover new disease-miRNA associations and to identify putative false associations reported in databases.

q-bio.QM↗

arXiv2016

A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm

We present a novel method that predicts transmembrane domains in proteins using solely information contained in the sequence itself. The PRED-TMR algorithm described, refines a standard hydrophobicity analysis with a detection of potential termini ('edges', starts and ends) of transmembrane regions. This allows one both to discard highly hydrophobic regions not delimited by clear start and end configurations and to confirm putative transmembrane segments not distinguishable by their hydrophobic composition. The accuracy obtained on a test set of 101 non-homologous transmembrane proteins with reliable topologies compares well with that of other popular existing methods. Only a slight decrease in prediction accuracy was observed when the algorithm was applied to all transmembrane proteins of the SwissProt database (release 35). A WWW server running the PRED-TMR algorithm is available at http://o2.db.uoa. gr/PRED-TMR/

q-bio.QM↗

arXiv2016

An hierarchical artificial neural network system for the classification of transmembrane proteins

This work presents a simple artificial neural network which classifies proteins into two classes from their sequences alone: the membrane protein class and the non-membrane protein class. This may be important in the functional assignment and analysis of open reading frames (ORF's) identified in complete genomes and, especially, those ORF's that correspond to proteins with unknown function. The network described here has a simple hierarchical feed-forward topology and a limited number of neurons which makes it very fast. By using only information contained in 11 protein sequences, the method was able to identify, with 100% accuracy, all membrane proteins with reliable topologies collected from several papers in the literature. Applied to a test set of 995 globular, water-soluble proteins, the neural network classified falsely 23 of them in the membrane protein class (97.7% of correct assignment). The method was also applied to the complete SWISS-PROT database with considerable success and on ORF's of several complete genomes. The neural network developed was associated with the PRED-TMR algorithm (Pasquier,C., Promponas,V.J., Palaios,G.A., Hamodrakas,J.S. and Hamodrakas,S.J., 1999) in a new application package called PRED-TMR2. A WWW server running the PRED-TMR2 software is available at http://o2.db.uoa.gr/PRED-TMR2

q-bio.QM↗

arXiv2010

Domain walls at the spin density wave endpoint of the organic superconductor (TMTSF)2PF6 under pressure

We report the first comprehensive investigation of the organic superconductor (TMTSF)2PF6 in the vicinity of the endpoint of the spin density wave - metal phase transition where phase coexistence occurs. At low temperature, the transition of metallic domains towards superconductivity is used to reveal the various textures. In particular, we demonstrate experimentally the existence of 1D and 2D metallic domains with a cross-over from a filamentary superconductivity mostly along the c?-axis to a 2D superconductivity in the b?c-plane perpendicular to the most conducting direction. The formation of these domain walls may be related to the proposal of a soliton phase in the vicinity of the critical pressure of the (TMTSF)2PF6 phase diagram.

cond-mat.str-el↗

arXiv2009

CoPreTHi: a Web tool which combines transmembrane protein segment prediction methods

CoPreTHi is a Java based web application, which combines the results of methods that predict the location of transmembrane segments in protein sequences into a joint prediction histogram. Clearly, the joint prediction algorithm, produces superior quality results than individual prediction schemes. The program is available at http://o2.db.uoa.gr/CoPreTHi

q-bio.QM↗

arXiv2009

A distributed editing environment for XML documents

XML is based on two essential aspects: the modelization of data in a tree like structure and the separation between the information itself and the way it is displayed. XML structures are easily serializable. The separation between an abstract representation and one or several views on it allows the elaboration of specialized interfaces to visualize or modify data. A lot of developments were made to interact with XML data but the use of these applications over the Internet is just starting. This paper presents a prototype of a distributed editing environment over the Internet. The key point of our system is the way user interactions are handled. Selections and modifications made by a user are not directly reflected on the concrete view, they are serialized in XML and transmitted to a server which applies them to the document and broadcasts updates to the views. This organization has several advantages. XML documents coding selection and modification operations are usually smaller than the edited document and can be directly processed with a transformation engine which can adapt them to different representations. In addition, several selections or modifications can be combined into an unique XML document. This allows one to update multiple views with different frequencies and fits the requirement of an asynchronous communication mode like HTTP.

cs.SE↗

arXiv2009

A web server to locate periodicities in a sequence

Summary : FT is a tool written in C++, which implements the Fourier analysis method to locate periodicities in aminoacid or DNA sequences. It is provided for free public use on a WWW server with a Java interface. Availability : The server address is http://o2.db.uoa.gr/FT Contact : shamodr@atlas.uoa.gr

q-bio.QM↗

arXiv2009

PRED-CLASS: cascading neural networks for generalized protein classification and genome-wide applications

A cascading system of hierarchical, artificial neural networks (named PRED-CLASS) is presented for the generalized classification of proteins into four distinct classes-transmembrane, fibrous, globular, and mixed-from information solely encoded in their amino acid sequences. The architecture of the individual component networks is kept very simple, reducing the number of free parameters (network synaptic weights) for faster training, improved generalization, and the avoidance of data overfitting. Capturing information from as few as 50 protein sequences spread among the four target classes (6 transmembrane, 10 fibrous, 13 globular, and 17 mixed), PRED-CLASS was able to obtain 371 correct predictions out of a set of 387 proteins (success rate approximately 96%) unambiguously assigned into one of the target classes. The application of PRED-CLASS to several test sets and complete proteomes of several organisms demonstrates that such a method could serve as a valuable tool in the annotation of genomic open reading frames with no functional assignment or as a preliminary step in fold recognition and ab initio structure prediction methods. Detailed results obtained for various data sets and completed genomes, along with a web sever running the PRED-CLASS algorithm, can be accessed over the World Wide Web at http://o2.biol.uoa.gr/PRED-CLASS

q-bio.QM↗

arXiv2009

Biological data integration using Semantic Web technologies

Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined. Semantic Web technologies, which provide a common framework allowing data to be shared and reused between applications, can be applied to the management of disseminated biological data. However, due to some specificities of biological data, the application of these technologies to life science constitutes a real challenge. Through a use case of biological data integration, we show in this paper that current Semantic Web technologies start to become mature and can be applied for the development of large applications. However, in order to get the best from these technologies, improvements are needed both at the level of tool performance and knowledge modeling.

q-bio.QM↗

arXiv2008

Magnetic-Field Variations of the Pair-Breaking Effects of Superconductivity in (TMTSF)2ClO4

We have studied the onset temperature of the superconductivity Tc_onset of the organic superconductor (TMTSF)2ClO4, by precisely controlling the direction of the magnetic field H. We compare the results of two samples with nearly the same onset temperature but with different scattering relaxation time tau. We revealed a complicated interplay of a variety of pair-breaking effects and mechanisms that overcome these pair-breaking effects. In low fields, the linear temperature dependences of the onset curves in the H-T phase diagrams are governed by the orbital pair-breaking effect. The dips in the in-plane field-angle phi dependence of Tc_onset, which were only observed in the long-tau sample, provides definitive evidence that the field-induced dimensional crossover enhances the superconductivity if the field direction is more than about 19-degrees away from the a axis. In the high-field regime for H//a, the upturn of the onset curve for the long-tau sample indicates a new superconducting state that overcomes the Pauli pair-breaking effect but is easily suppressed by impurity scatterings. The Pauli effect is also overcome for H//b' by a realization of another state for which the maximum of Tc_onset(phi) occurs in a direction different from the crystalline axes. The effect on Tc_onset of tilting the applied field out of the conductive plane suggests that the Pauli effect plays a significant role in determining Tc_onset. The most plausible explanation of these results is that (TMTSF)2ClO4 is a singlet superconductor and exhibits Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) states in high fields.

cond-mat.supr-con↗

arXiv2007

THEA: ontology-driven analysis of microarray data

MOTIVATION: Microarray technology makes it possible to measure thousands of variables and to compare their values under hundreds of conditions. Once microarray data are quantified, normalized and classified, the analysis phase is essentially a manual and subjective task based on visual inspection of classes in the light of the vast amount of information available. Currently, data interpretation clearly constitutes the bottleneck of such analyses and there is an obvious need for tools able to fill the gap between data processed with mathematical methods and existing biological knowledge. RESULTS: THEA (Tools for High-throughput Experiments Analysis) is an integrated information processing system allowing convenient handling of data. It allows to automatically annotate data issued from classification systems with selected biological information coming from a knowledge base and to either manually search and browse through these annotations or automatically generate meaningful generalizations according to statistical criteria (data mining). AVAILABILITY: The software is available on the website http://thea.unice.fr/

q-bio.QM↗

arXiv2005

Impurity controlled Superconductivity/Spin Density Wave interplay in the organic superconductor : (TMTSF)\_2ClO\_4

The study of the anion ordered (TMTSF)\_2ClO\_4\_(1-x)ReO\_4\_x, solid solution in the limit of a low ReO\_4- substitution level (0<=x<=17%) has revealed a new and interesting phase diagram. Superconductivity is drastically suppressed as the effect of ReO\_4- non magnetic point defects increases following the digamma behaviour for usual superconductors in the presence of paramagnetic impurities. Then, no long range order can be stabilized above 0.1K in a narrow window of substitution. Finally, an insulating SDW ground state in ReO\_4- -rich samples is rapidly stabilized with the decrease of the potential strength leading to the doubling of the transverse periodicity. This extensive study has shown that the superconducting order parameter must change its sign over the Fermi surface.

cond-mat.supr-con↗

arXiv2004

Suppression of superconductivity by non-magnetic disorder in the organic superconductor (TMTSF)2(ClO4)(1-x)(ReO4)x

We present a study of the superconducting properties (Tc and Hc2) in the solid solution (TMTSF)2(ClO4)(1-x)(ReO4)x with a ReO-4 nominal concentration up to x = 6%. The dramatic suppression of Tc when the residual resistivity is increased upon alloying with no modification of the Fermi surface is the signature of non-conventional superconductivity . This behaviour strongly supports p or d wave pairing in quasi one dimensional organic superconductors. The determination of the electron lifetime in the normal state at low temperature confirms that a single particle Drude model is unable to explain the temperature dependence of the conductivity and that a very narrow zero frequency mode must be taken into account for the interpretation of the transport properties.

cond-mat.supr-con↗

arXiv2002

Scanning Tunneling Microscopy in TTF-TCNQ :direct proof of phase and amplitude modulated charge density waves

Charge density waves (CDW) have been studied at the surface of a cleaved TTF-TCNQ single crystal using a low temperature scanning tunneling microscope (STM) under ultra high vacuum (UHV) conditions. All CDW phase transitions of TTF-TCNQ have been identified. The measurement of the modulation wave vector along the a direction provides the first evidence for the existence of domains comprising single plane wave modulated structures in the temperature regime where the transverse wave vector of the CDW is temperature dependent, as hinted by the theory more than 20 years ago.

cond-mat.str-el↗