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Determination of specificity influencing residues for key transcription factor families

Frontiers of Electrical and Electronic Engineering in China 2015年第3期10卷 115-123页

作者： Ronak Y Patel christian garde Gary D Stormo Department of Genetics School of Medicine Washington University St. Louis MO 63108 USA. Center for Biological Sequence Analysis Department of Systems Biology Technical University of Denmark Kgs. Lyngby DK 2800 Denmark.

Transcription factors （TFs） are major modulators of transcription and subsequent cellular processes. The binding of TFs to specific regulatory elements is governed by their specificity. Considering the gap between known TFs sequence and specificity, specificity prediction frameworks are highly desired. Key inputs to such frameworks are protein residues that modulate the specificity of TF under consideration. Simple measures like mutual information （MI） to delineate specificity influencing residues （SIRs） from alignment fail due to structural constraints imposed by the three-dimensional structure of protein. Structural restraints on the evolution of the amino-acid sequence lead to identification of false SIRs. In this manuscript we extended three methods （direct information, PSICOV and adjusted mutual information） that have been used to disentangle spurious indirect protein residue-residue contacts from direct contacts, to identify SIRs from joint alignments of amino-acids and specificity. We predicted SIRs for homeodomain （HI））, helix-loop-helix, LacI and GntR families of TFs using these methods and compared to MI. Using various measures, we show that the performance of these three methods is comparable but better than MI. Implication of these methods in specificity prediction framework is discussed. The methods are implemented as an R package and available along with the alignments at http：//***/SpecPred.

关键词： protein-DNA interactions residue co-variance motifs co-evolution feature selection direct information specificity determinants

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A mathematical model in closed for unsteady mixed flows water pipes Dedicated to the NSFC-CNRS Chinese-French summer institute on fluid mechanics in 2010

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Science China Mathematics 2012年第2期55卷 221-244页

作者： BOURDARIAS christian ERSOY Mehmet GERBI Stephane Laboratoire de Mathdmatiques Universitd de Savoie Le Bourget du Lac 73376 France Basque Center for Applied Mathematics Bizkaia Technology Park Derio Basque Country 48160 Spain Institut des Mathematiques de Toulon et du Vat Universite du Sud Toulon-Var La Garde Cedex 83957 France

We present the formal derivation of a new unidirectional model for unsteady mixed flows in nonuniform closed water pipes. In the case of free surface incompressible flows, the FS-model is formally obtained, using formal asymptotic analysis, which is an extension to more classical shallow water models. In the same way, when the pipe is full, we propose the P-model, which describes the evolution of a compressible inviscid flow, close to gas dynamics equations in a nozzle. In order to cope with the transition between a free surface state and a pressured （i.e., compressible） state, we propose a mixed model, the PFS-model, taking into account changes of section and slope variation.

关键词： shallow water equations unsteady mixed flows free surface flows pressurized flows curvilinear transformation asymptotic analysis

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