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Computational biology

Related publications (422)

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Low inhibiting power of N...CO based peptidomimetic compounds against HIV protease: Insights from a hybrid QM/MM study

Ursula Röthlisberger, Michele Cascella

Recently, Hasserodt et al. proposed new HIV-1 drug candidates based on a weak N center dot center dot center dot CO interaction, designed to be a close transition state analog (Gautier et al. Bioorg. Med. Chem. 2006, 14, 3835-3847; Waibel et al. J. Bioorg. ...

2010

Quantitative Analysis of Robustness in Systems Biology

Marc Hafner

To characterize the behavior and robustness of cellular circuits is a major challenge for Systems Biology. Many of the published methods that address this question quantify the local robustness of the models. In this thesis, I tried to underpin the inappro ...

EPFL2010

3D RANS computations of open channel flows with a sharp bend

Koen Blanckaert

This paper describes a 3D computation of an open channel flow with a sharp bend. The flow with a bend is characterized by generation of secondary current of the first kind due to the local unbalance of the centrifugal force and lateral pressure gradient. S ...

2010

Recursive column generation for the Tactical Berth Allocation Problem

Michel Bierlaire, Matteo Salani, Ilaria Vacca

Seaport container terminals are source of many interesting large-scale optimization problems, that arise in the management of operations at several decision levels. In this work we study exact methods to solve the Tactical Berth Allocation Problem with Qua ...

2010

Processing and analyzing ChIP-seq data: from short reads to regulatory interactions

Jacques Rougemont, Marion Leleu

Chromatin-immunoprecipitation and sequencing (ChIP-seq) is a rapidly maturing technology that draws on the power of high-throughput short-read sequencing to decipher chromatin states with unprecedented precision and breadth. Although some aspects of the ex ...

2010

Dopamine Adsorption on Anatase TiO2(101): A Photoemission and NEXAFS Spectroscopy Study

The adsorption of dopamine onto an anatase TiO2(101) single crystal has been studied using photoemission and NEXAFS techniques Photoemission Jesuits suggest that the dopamine molecule adsorbs on the surface in a bidentate geometry, resulting in the removal ...

American Chemical Society2010

DREAMS of metabolism

Vassily Hatzimanikatis, Keng Cher Soh

Metabolic networks have been studied for decades, and sophisticated computational frameworks are needed to augment experimental approaches to harness these complex networks. BNICE (Biochemical Network Integrated Computational Explorer), a computational app ...

Elsevier2010

Fast Adaptive Uniformization for the Chemical Master Equation

Maria-Emanuela-Canini Mateescu, Verena Wolf

Within systems biology there is an increasing interest in the stochastic behavior of biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous-time Markov chain (CTMC). S ...

Ieee Computer Soc Press, Customer Service Center, Po Box 3014, 10662 Los Vaqueros Circle, Los Alamitos, Ca 90720-1264 Usa2009

Implicit methods for modeling gene regulatory networks

Abhishek Garg

Advancements in high-throughput technologies to measure increasingly complex biological phenomena at the genomic level are rapidly changing the face of biological research from single-gene single-protein experimental approach to studying the behaviour of a ...

EPFL2009

Integration column: Microfluidic high-throughput screening

Sebastian Maerkl

Biology has always been a heavily technology limited field. Burgeoning fields such as systems biology require the development and implementation of new technologies, enabling high-throughput and high-fidelity measurements of large systems. Microfluidics pr ...

2009