8 years 8 months ago
The PathOlogist: An Automated Tool for Pathway-Centric Analysis
Background: The PathOlogist is a new tool designed to transform large sets of gene expression data into quantitative descriptors of pathway-level behavior. The tool aims to provid...
Sharon I. Greenblum, Sol Efroni, Carl F. Schaefer,...
129views more  SCFBM 2008»
9 years 1 months ago
Faunus: An object oriented framework for molecular simulation
Background: We present a C++ class library for Monte Carlo simulation of molecular systems, including proteins in solution. The design is generic and highly modular, enabling mult...
Mikael Lund, Martin Trulsson, Björn Persson
88views more  JCC 2002»
9 years 1 months ago
Pattern recognition strategies for molecular surfaces. I. Pattern generation using fuzzy set theory
: A new method for the characterization of molecules based on the model approach of molecular surfaces is presented. We use the topographical properties of the surface as well as t...
Thomas E. Exner, Matthias Keil, Jürgen Brickm...
117views more  BMCBI 2004»
9 years 2 months ago
Cancer characterization and feature set extraction by discriminative margin clustering
Background: A central challenge in the molecular diagnosis and treatment of cancer is to define a set of molecular features that, taken together, distinguish a given cancer, or ty...
Kamesh Munagala, Robert Tibshirani, Patrick O. Bro...
151views more  BMCBI 2005»
9 years 2 months ago
stam - a Bioconductor compliant R package for structured analysis of microarray data
Background: Genome wide microarray studies have the potential to unveil novel disease entities. Clinically homogeneous groups of patients can have diverse gene expression profiles...
Claudio Lottaz, Rainer Spang
69views more  IWC 2006»
9 years 2 months ago
An overview of auditory display to assist comprehension of molecular information
This paper presents an overview of auditory display (the use of non-speech sounds to convey information) applied to the study of molecular properties in human
Miguel Angel Garcia-Ruiz, Jorge Rafael Gutierrez-P...
9 years 2 months ago
A multiscale systems approach to microelectronic processes
This paper describes applications of molecular simulation to microelectronics processes and the subsequent development of techniques for multiscale simulation and multiscale syste...
Richard D. Braatz, Richard C. Alkire, Edmund G. Se...
69views Education» more  CORR 2010»
9 years 2 months ago
A simple model for the evolution of molecular codes driven by the interplay of accuracy, diversity and cost
Molecular codes translate information written in one type of molecule into another molecular language. We introduce a simple model that treats molecular codes as noisy information...
Tsvi Tlusty
135views Education» more  CORR 2010»
9 years 2 months ago
The Power of Nondeterminism in Self-Assembly
tigate the role of nondeterminism in Winfree's abstract Tile Assembly Model (aTAM), which was conceived to model artificial molecular self-assembling systems constructed from...
Nathaniel Bryans, Ehsan Chiniforooshan, David Doty...
143views more  CGF 2010»
9 years 2 months ago
Coherent Culling and Shading for Large Molecular Dynamics Visualization
Molecular dynamics simulations are a principal tool for studying molecular systems. Such simulations are used to investigate molecular structure, dynamics, and thermodynamical pro...
Sebastian Grottel, Guido Reina, Carsten Dachsbache...