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- Bettina Knapp, Ilka Rebhan, Anil Kumar, Petr Matula, Narsis A Kiani, Marco Binder +5 others
- BMC Bioinformatics
- 2011

BACKGROUND
High-content, high-throughput RNA interference (RNAi) offers unprecedented possibilities to elucidate gene function and involvement in biological processes. Microscopy based screening allows phenotypic observations at the level of individual cells. It was recently shown that a cell's population context significantly influences results. However,… (More)

- David Gomez-Cabrero, Jörg Menche, Isaac Cano, Imad Abugessaisa, Mercedes Huertas-Migueláñez, Akos Tenyi +12 others
- Journal of Translational Medicine
- 2014

Chronic Obstructive Pulmonary Disease (COPD) patients are characterized by heterogeneous clinical manifestations and patterns of disease progression. Two major factors that can be used to identify COPD subtypes are muscle dysfunction/wasting and co-morbidity patterns. We hypothesized that COPD heterogeneity is in part the result of complex interactions… (More)

To cope with the complexity of large networks, a number of dimen-sionality reduction techniques for graphs have been developed. However , the extent to which information is lost or preserved when these techniques are employed has not yet been clear. Here we develop a framework, based on algorithmic information theory, to quantify the extent to which… (More)

We undertake an extensive numerical investigation of the graph spectra of thousands regular graphs, a set of random Erdös-Rényi graphs, the two most popular types of complex networks and an evolving genetic network by using novel conceptual and experimental tools. Our objective in so doing is to contribute to an understanding of the meaning of the… (More)

Network inference deals with the reconstruction of molecular networks from experimental data. Given N molecular species, the challenge is to find the underlying network. Due to data limitations, this typically is an ill-posed problem, and requires the integration of prior biological knowledge or strong regularization. We here focus on the situation when… (More)

We survey and introduce concepts and tools located at the intersection of information theory and network biology. We show that Shannon's information entropy, compressibility and algorithmic complexity quantify different local and global aspects of synthetic and biological data. We show examples such as the emergence of giant components in Erdös-Rényi random… (More)

A common practice in the estimation of the complexity of objects, in particular of graphs, is to rely on graph- and information-theoretic measures. Here, using integer sequences with properties such as Borel normality, we explain how these measures are not independent of the way in which a single object, such a graph, can be described. From descriptions… (More)

Network inference is a rapidly advancing field, with new methods being proposed on a regular basis. Understanding the advantages and limitations of different network inference methods is key to their effective application in different circumstances. The common structural properties shared by diverse networks naturally pose a challenge when it comes to… (More)

We investigate the properties of a divide-and-conquer Block Decomposition Method (BDM), which extends the power of a Coding Theorem Method (CTM) that approximates local estimations of algorithmic complexity and of logical depth based upon Solomonoff-Levin's theory of algorithmic probability, thereby providing a closer connection to algorithmic complexity.… (More)