84,189 research outputs found
Visual and computational analysis of structure-activity relationships in high-throughput screening data
Novel analytic methods are required to assimilate the large volumes of structural and bioassay data generated by combinatorial chemistry and high-throughput screening programmes in the pharmaceutical and agrochemical industries. This paper reviews recent work in visualisation and data mining that can be used to develop structure-activity relationships from such chemical/biological datasets
A biophysical approach to large-scale protein-DNA binding data
About this book * Cutting-edge genome analysis methods from leading bioinformaticians An accurate description of current scientific developments in the field of bioinformatics and computational implementation is presented by research of the BioSapiens Network of Excellence. Bioinformatics is essential for annotating the structure and function of genes, proteins and the analysis of complete genomes and to molecular biology and biochemistry. Included is an overview of bioinformatics, the full spectrum of genome annotation approaches including; genome analysis and gene prediction, gene regulation analysis and expression, genome variation and QTL analysis, large scale protein annotation of function and structure, annotation and prediction of protein interactions, and the organization and annotation of molecular networks and biochemical pathways. Also covered is a technical framework to organize and represent genome data using the DAS technology and work in the annotation of two large genomic sets: HIV/HCV viral genomes and splicing alternatives potentially encoded in 1% of the human genome
ILR Faculty Research in Progress, 2015-2016
The production of scholarly research continues to be one of the primary missions of the ILR School. During a typical academic year, ILR faculty members published or had accepted for publication over 25 books, edited volumes, and monographs, 170 articles and chapters in edited volumes, numerous book reviews. In addition, a large number of manuscripts were submitted for publication, presented at professional association meetings, or circulated in working paper form. Our faculty's research continues to find its way into the very best industrial relations, social science and statistics journals.ResearchinProgress_2015_16.pdf: 22 downloads, before Oct. 1, 2020
Time-Space Efficient Regression Testing for Configurable Systems
Configurable systems are those that can be adapted from a set of options.
They are prevalent and testing them is important and challenging. Existing
approaches for testing configurable systems are either unsound (i.e., they can
miss fault-revealing configurations) or do not scale. This paper proposes
EvoSPLat, a regression testing technique for configurable systems. EvoSPLat
builds on our previously-developed technique, SPLat, which explores all
dynamically reachable configurations from a test. EvoSPLat is tuned for two
scenarios of use in regression testing: Regression Configuration Selection
(RCS) and Regression Test Selection (RTS). EvoSPLat for RCS prunes
configurations (not tests) that are not impacted by changes whereas EvoSPLat
for RTS prunes tests (not configurations) which are not impacted by changes.
Handling both scenarios in the context of evolution is important. Experimental
results show that EvoSPLat is promising. We observed a substantial reduction in
time (22%) and in the number of configurations (45%) for configurable Java
programs. In a case study on a large real-world configurable system (GCC),
EvoSPLat reduced 35% of the running time. Comparing EvoSPLat with sampling
techniques, 2-wise was the most efficient technique, but it missed two bugs
whereas EvoSPLat detected all bugs four times faster than 6-wise, on average.Comment: 14 page
ILR Research in Progress 2011-12
The production of scholarly research continues to be one of the primary missions of the ILR School. During a typical academic year, ILR faculty members published or had accepted for publication over 25 books, edited volumes, and monographs, 170 articles and chapters in edited volumes, numerous book reviews. In addition, a large number of manuscripts were submitted for publication, presented at professional association meetings, or circulated in working paper form. Our faculty's research continues to find its way into the very best industrial relations, social science and statistics journals.Research_in_Progress_2011_12.pdf: 46 downloads, before Oct. 1, 2020
PRED-CLASS: cascading neural networks for generalized protein classification and genome-wide applications
A cascading system of hierarchical, artificial neural networks (named
PRED-CLASS) is presented for the generalized classification of proteins into
four distinct classes-transmembrane, fibrous, globular, and mixed-from
information solely encoded in their amino acid sequences. The architecture of
the individual component networks is kept very simple, reducing the number of
free parameters (network synaptic weights) for faster training, improved
generalization, and the avoidance of data overfitting. Capturing information
from as few as 50 protein sequences spread among the four target classes (6
transmembrane, 10 fibrous, 13 globular, and 17 mixed), PRED-CLASS was able to
obtain 371 correct predictions out of a set of 387 proteins (success rate
approximately 96%) unambiguously assigned into one of the target classes. The
application of PRED-CLASS to several test sets and complete proteomes of
several organisms demonstrates that such a method could serve as a valuable
tool in the annotation of genomic open reading frames with no functional
assignment or as a preliminary step in fold recognition and ab initio structure
prediction methods. Detailed results obtained for various data sets and
completed genomes, along with a web sever running the PRED-CLASS algorithm, can
be accessed over the World Wide Web at http://o2.biol.uoa.gr/PRED-CLAS
ILR Research in Progress 2013-14
The production of scholarly research continues to be one of the primary missions of the ILR School. During a typical academic year, ILR faculty members published or had accepted for publication over 25 books, edited volumes, and monographs, 170 articles and chapters in edited volumes, numerous book reviews. In addition, a large number of manuscripts were submitted for publication, presented at professional association meetings, or circulated in working paper form. Our faculty's research continues to find its way into the very best industrial relations, social science and statistics journals.Research_in_Progress_2013_14.pdf: 54 downloads, before Oct. 1, 2020
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