Publications by Daniel Marbach

Beyond Graphs: A New Synthesis

Dario Floreano, Daniel Marbach, Claudio Mattiussi, Peter Dürr

Artiﬁcial neural networks, electronic circuits, and gene networks are some examples of systems that can be modeled as networks, that is, as collections of interconnected nodes. In this paper we introduce the concept of terminal graph (t-graph for short), w ...

2011

GeneNetWeaver: In silico benchmark generation and performance profiling of network inference methods

Dario Floreano, Daniel Marbach, Thomas Schaffter

Motivation: Over the last decade, numerous methods have been developed for inference of regulatory networks from gene expression data. However, accurate and systematic evaluation of these methods is hampered by the difficulty of constructing adequate bench ...

Oxford University Press2011

Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges

Daniel Marbach

Background: Systems biology has embraced computational modeling in response to the quantitative nature and increasing scale of contemporary data sets. The onslaught of data is accelerating as molecular profiling technology evolves. The Dialogue for Reverse ...

Public Library of Science2010

Evolutionary reverse engineering of gene networks

Daniel Marbach

The expression of genes is controlled by regulatory networks, which perform fundamental information processing and control mechanisms in a cell. Unraveling and modelling these networks will be indispensable to gain a systems-level understanding of biologic ...

EPFL2009

Replaying the Evolutionary Tape: Biomimetic Reverse Engineering of Gene Networks

Dario Floreano, Daniel Marbach, Claudio Mattiussi

In this paper, we suggest a new approach for reverse engineering gene regulatory networks, which consists of using a reconstruction process that is similar to the evolutionary process that created these networks. The aim is to integrate prior knowledge int ...

Blackwell Publishing, 9600 Garsington Rd, Oxford Ox4 2Dq, Oxen, England2009

Generating Realistic In Silico Gene Networks for Performance Assessment of Reverse Engineering Methods

Dario Floreano, Daniel Marbach, Claudio Mattiussi, Thomas Schaffter

Reverse engineering methods are typically first tested on simulated data from in silico networks, for systematic and efficient performance assessment, before an application to real biological networks. In this paper we present a method for generating biolo ...

2009

Combining Multiple Results of a Reverse Engineering Algorithm: Application to the DREAM Five Gene Network Challenge

Dario Floreano, Daniel Marbach, Claudio Mattiussi

The output of reverse engineering methods for biological networks is often not a single network prediction, but an ensemble of networks that are consistent with the experimentally measured data. In this paper, we consider the problem of combining the infor ...

Blackwell Publishing, 9600 Garsington Rd, Oxford Ox4 2Dq, Oxen, England2009

The Age of Analog Networks

Dario Floreano, Daniel Marbach, Claudio Mattiussi, Peter Dürr

A large class of systems of biological and technological relevance can be described as analog networks, that is, collections of dynamical devices interconnected by links of varying strength. Some examples of analog networks are genetic regulatory networks, ...

2008

Bio-mimetic Evolutionary Reverse Engineering of Genetic Regulatory Networks

Dario Floreano, Daniel Marbach, Claudio Mattiussi

The effective reverse engineering of biochemical networks is one of the great challenges of systems biology. The contribution of this paper is two-fold: 1) We introduce a new method for reverse engineering genetic regulatory networks from gene expression d ...

Springer-Verlag Berlin2007