Reconstructing neuronal circuits at the level of synapses is a central problem in neuroscience and becoming a focus of the emerging field of connectomics. To date, electron microscopy (EM) is the most proven technique for identifying and quantifying synaptic connections. As advances in EM make acquiring larger datasets possible, subsequent manual synapse identification (i.e., proofreading) for ...

This paper summarizes the gains expected for vector entomology from the acquisition of the genome sequence of disease-transmitting arthropods. The results of this kind of high-throughput science, especially the direct consequences that could be summarily described as post-genomic activities, may lead to a better understanding of the biology of the vectors, including population studies, interact...

Summary: Identifying gene co-expression is a significant step in understanding functional relationships between genes. Existing methods primarily depend on analyses of correlation between pairs of genes; however, this neglects structural elements between experimental conditions. We present a novel approach to identifying clusters of co-expressed genes that incorporates these structures. Availab...

As John Muir noted, “When we try to pick out anything by itself, we find it hitched to everything else in the Universe” (Muir, 1911). In tune with Muir’s elegantly stated notion, research in molecular biology is progressing toward a systems level approach, with a goal of modeling biological systems at the molecular level. To achieve such a lofty goal, the analysis of multiple datasets is requir...

The modern high-throughput sequencing methods provide massive amounts of genome-focused, DNA-positioned data. This data is often represented as a function of the DNA coordinate (e.g. coverage). The genomeor chromosome-wide correlations between data from different sources may provide information about functional biological interrelation of the investigated features, e.g., trancription and histon...

In this paper, we investigate the differences and similarities in user job submission behavior in High Performance Computing (HPC) and High Throughput Computing (HTC). We consider job submission behavior in terms of parallel batch-wise submissions, as well as delays and pauses in job submission. Our findings show that modeling user-based HTC job submission behavior requires knowledge of the und...

SUMMARY The accurate mass and time (AMT) tag approach is used for analysis of large scale experiments by combining information generated over multiple datasets and instrument types. The VIPER software package is one of the key components of the data processing pipeline and implements automated algorithms to discover LC-MS features, align and match these LC-MS features to a database of peptides ...

DNA sequencing using reversible terminators, as one sequencing by synthesis strategy, has garnered a great deal of interest due to its popular application in the second-generation high-throughput DNA sequencing technology. In this review, we provided its history of development, classification, and working mechanism of this technology. We also outlined the screening strategies for DNA polymerase...

Received 25 September 2002; revised 22 October 2002; accepted 27 November 2002. For correspondence (fax þ6 351 7050; e-mail [email protected]). yPresent address: Crop and Food Research, Private Bag 11600, Palmerston North, New Zealand. zPresent address: Sygen International, Suite 130, 2929 Seventh Street, Berkeley, CA 94710, USA. Present address: Molecular Biology Department, University of ...

A variety of high-throughput methods have made it possible to generate detailed temporal expression data for a single gene or large numbers of genes. Common methods for analysis of these large data sets can be problematic. One challenge is the comparison of temporal expression data obtained from different growth conditions where the patterns of expression may be shifted in time. We propose the ...