Graph theoretical approach to study eQTL: a case study of Plasmodium falciparum (2009)
Huang, Yang, Wuchty, Stefan, Ferdig, Michael T., Przytycka, Teresa M.
Motivation: Analysis of expression quantitative trait loci (eQTL) significantly contributes to the determination of gene regulation programs. However, the discovery and analysis of associations of...
Regulatory Hotspots in the Malaria Parasite Genome Dictate Transcriptional Variation (2008)
Joseph M. Gonzales, Jigar J. Patel, Napawan Ponmee, Lei Jiang, Asako Tan, Steven P. Maher, ...
The determinants of transcriptional regulation in malaria parasites remain elusive. The presence of a well-characterized gene expression cascade shared by different Plasmodium falciparum strains...
Viral organization of human proteins (2008)
A compilation of experimentally verified interactions between HIV-1 and human proteins allows insights into the intricate interplay between viral and host proteins on a large scale.We find that HIV-1...
Chengbang Huang, Simon P. Kanaan, Stefan Wuchty, Danny Z. Chen, Jesús A. Izaguirre
The goal of contemporary proteome research is the elucidation of protein interactions in the cell. Based on cur-rently available protein-protein interaction and domain data of S. cerevisiae, we...
Predicting protein-protein interactions from protein domains using a set cover approach (2007)
Chengbang Huang, Faruck Morcos, Simon P. Kanaan, Stefan Wuchty, Danny Z. Chen, Jesús A. Izaguirre
Abstract—One goal of contemporary proteome research is the elucidation of cellular protein interactions. Based on currently available protein-protein interaction and domain data, we introduce a...
Predicting protein-protein interactions from protein domains using a set cover approach (2007)
Chengbang Huang, Faruck Morcos, Simon P. Kanaan, Stefan Wuchty, Danny Z. Chen, Jesús A. Izaguirre
Abstract—One goal of contemporary proteome research is the elucidation of cellular protein interactions. Based on currently available protein-protein interaction and domain data, we introduce a...
Abstract Background While the analysis of unweighted biological webs as diverse as genetic, protein and metabolic networks allowed spectacular insights in the inner workings of a cell, biological...
Stable evolutionary signal in a Yeast protein interaction network (2006)
Wuchty, Stefan, Barabási, Albert-Laszlo, Ferdig, Michael T
Abstract Background The recently emerged protein interaction network paradigm can provide novel and important insights into the innerworkings of a cell. Yet, the heavy burden of both false positive...
Stefan Wuchty, Albert-laszlo Barabási
Background: The recently emerged protein interaction network paradigm can provide novel and important insights into the innerworkings of a cell. Yet, the heavy burden of both false positive and false...
BMC Genomics BioMed Central (2006)
Research article Topology and weights in a protein domain interaction network – a novel way to predict protein interactions
Evolutionary cores of domain co-occurrence networks (2005)
Wuchty, Stefan, Almaas, Eivind
Abstract Background The modeling of complex systems, as disparate as the World Wide Web and the cellular metabolism, as networks has recently uncovered a set of generic organizing principles: Most of...
Evolution and Topology in the Yeast Protein Interaction Network (2004)
The integrity of the yeast protein–protein interaction network is maintained by a few highly connected proteins, or hubs, which hold the numerous less-connected proteins together. The structural...
The architecture of biological networks (2003)
Stefan Wuchty, Erszébet Ravasz, Albert-lászló Barabási
Understanding complex systems often requires a bottom-up approach, breaking the system into small and elementary constituents and mapping out the interactions be-tween these components. In many...
Centers of complex networks (2003)
Stefan Wuchty, Peter F. Stadler
Abstract. The central vertices in complex networks are of particular interest because they might play the role of organizational hubs. Here, we consider three different geometric centrality measures,...
Centers of Complex Networks (2003)
Stefan Wuchty, Peter F. Stadler
The central vertices in complex networks are of particular interest because they might play the role of organizational hubs. Here, we consider three di#erent geometric centrality measures,...
Small worlds in RNA structures (2003)
I consider conformational spaces of tRNAphe defined by sets of suboptimal structures from the perspective of small‐world networks. Herein, the influence of modifications on typical...
DOI: 10.1093/nar/gkg162 Small worlds in RNA structures (2002)
I consider conformational spaces of tRNAphe de®ned by sets of suboptimal structures from the perspective of small-world networks. Herein, the in¯uence of modi®cations on typical small-world...
Scale-Free Behavior in Protein Domain Networks (2001)
Several technical, social, and biological networks were recently found to demonstrate scale-free and small-world behavior instead of random graph characteristics. In this work, the topology of...
Complete Suboptimal Folding of RNA and the Stability of Secondary Structures (1998)
Stefan Wuchty, Walter Fontana, Ivo L. Hofacker, Peter Schuster
An algorithm is presented for generating rigorously all suboptimal secondary structures between the minimum free energy and an arbitrary upper limit. The algorithm is particularly fast in the...
Complete Suboptimal Folding of RNA and the Stability of Secondary Structures (1998)
Stefan Wuchty, Walter Fontana, Ivo L. Hofacker, Peter Schuster
this paper we describe a fairly simple algorithm which generates all suboptimal folds of a sequence within a desired energy range from the mfe. The idea underlying the algorithm is straightforward,...
Complete Suboptimal Folding of RNA and the Stability of Secondary Structures (1998)
Stefan Wuchty, Walter Fontana, Ivo L. Hofacker, Peter Schuster
this paper we describe a fairly simple algorithm which generates all suboptimal folds of a sequence within a desired energy range from the mfe. The idea underlying the algorithm is straightforward,...
The Increasing Dominance of Teams in Production of Knowledge (1036)
G. G. Simpson, C. Dean, L. Corbesier, G. Coupl, Plant Cell Environ, T. Imaizumi, ...
(1976).
Small worlds in RNA structures
I consider conformational spaces of tRNAphe defined by sets of suboptimal structures from the perspective of small-world networks. Herein, the influence of modifications on typical small-world...
Evolution and Topology in the Yeast Protein Interaction Network
The integrity of the yeast protein–protein interaction network is maintained by a few highly connected proteins, or hubs, which hold the numerous less-connected proteins together. The structural...
Small worlds in RNA structures
I consider conformational spaces of tRNAphe defined by sets of suboptimal structures from the perspective of small-world networks. Herein, the influence of modifications on typical small-world...
Evolution and Topology in the Yeast Protein Interaction Network
The integrity of the yeast protein–protein interaction network is maintained by a few highly connected proteins, or hubs, which hold the numerous less-connected proteins together. The structural...
Complete Suboptimal Folding of RNA and the Stability of Secondary Structures
Stefan Wuchty, Walter Fontana, Ivo L. Hofacker, Peter Schuster
An algorithm is presented for generating rigorously all suboptimal secondary structures between the minimum free energy and an arbitrary upper limit. The algorithm performs particularly well in the...
Recent advances have provided a first experimental protein interaction map of the human malaria parasite P. falciparum, which appears to be remotely related to interactomes of other eukaryotes. Here,...
Regulatory Hotspots in the Malaria Parasite Genome Dictate Transcriptional Variation
Gonzales, Joseph M, Patel, Jigar J, Ponmee, Napawan, Jiang, Lei, Tan, Asako, Maher, Steven P, ...
The determinants of transcriptional regulation in malaria parasites remain elusive. The presence of a well-characterized gene expression cascade shared by different Plasmodium falciparum strains...
Graph theoretical approach to study eQTL: a case study of Plasmodium falciparum
Huang, Yang, Wuchty, Stefan, Ferdig, Michael T., Przytycka, Teresa M.
Motivation: Analysis of expression quantitative trait loci (eQTL) significantly contributes to the determination of gene regulation programs. However, the discovery and analysis of associations of...