Purpose: Describe a high-throughput method for the analysis of uncertain models, e.g. in biological research. Methods: Generalized modeling for conceptual analysis of large classes of models. Results: Local dynamics of uncertain networks are revealed as a function of intuitive parameters. Conclusions: Generalized modeling easily scales to very large networks.

SUMMARY We present LOX (Level Of eXpression) that estimates the Level Of gene eXpression from high-throughput-expressed sequence datasets with multiple treatments or samples. Unlike most analyses, LOX incorporates a gene bias model that facilitates integration of diverse transcriptomic sequencing data that arises when transcriptomic data have been produced using diverse experimental methodologi...

Biomarkers are playing an increasingly important role in drug discovery and development and can be applied for many purposes, including disease mechanism study, diagnosis, prognosis, staging, and treatment selection. Advances in high-throughput “omics” technologies, including genomics, transcriptomics, proteomics and metabolomics, significantly accelerate the pace of biomarker discovery. Compre...

Heterogeneity and latent variables are now widely recognized as major sources of bias and variability in high-throughput experiments. The most well-known source of latent variation in genomic experiments are batch effects-when samples are processed on different days, in different groups or by different people. However, there are also a large number of other variables that may have a major impac...

Biomedical research has been revolutionized by high-throughput techniques and the enormous amount of biological data they are able to generate. The interest shown over network models and systems biology is rapidly raising. Genetic networks arise as an essential task to mine these data since they explain the function of genes in terms of how they influence other genes. Many modeling approaches h...

This paper presents the design of a high-throughput, low-latency, asP*, RGD arbiter. Spice simulations for an implementation in a 0:8 CMOS process show a request-to-grant delay of 0:74ns and a done-to-grant-delay of 0:4ns. Maximum throughput of requests from a single client is one grant per 1:8ns; if both clients make request aggressively, the arbiter can produce one grant per 1:2ns. In additio...

A reliable multicast protocol enables a process to multicast a message to a group of processes in a way that ensures that all honest destination-group members receive the same message, even if some group members and the multicast initiatorare maliciously faulty. Reliable multicast has been shown to be useful for building multiparty cryptographic protocols and secure distributed services. We pre...

How best to design and redesign high-throughput experiments for zeolite synthesis is addressed. A model that relates materials function to chemical composition of the zeolite and the structure directing agent is introduced. Using this model, several Monte Carlo-like design protocols are evaluated. Multi-round protocols are found to be effective, and strategies that use a priori information abou...

Abstract: In this vignette, we demonstrate the application of KEGGprofile as an annotation and visualization tool in analysis of multi-types and multi-groups high-throughput expression data. Superior to existing approaches, KEGGprofile combined the KEGG pathway map with expression profiles of genes in that pathway and facilitated more detailed analysis about the specific function changes inner ...

Supplementary Data High-fidelity gene synthesis by retrieval of sequence verified DNA identified using high-throughput pyrosequencing Mark Matzas*, Peer F. Stähler*, Nathalie Kefer, Nicole Siebelt, Valesca Boisguérin, Jack T. Leonard, Andreas Keller, Cord F. Stähler, Pamela Häberle, Baback Gharizadeh, Farbod Babrzadeh, George Church febit group, Im Neuenheimer Feld 519, 69121 Heidelberg, German...