21,972 research outputs found
Enhanced maps of transcription factor binding sites improve regulatory networks learned from accessible chromatin data
Determining where transcription factors (TFs) bind in genomes provides insight into which transcriptional programs are active across organs, tissue types, and environmental conditions. Recent advances in high-throughput profiling of regulatory DNA have yielded large amounts of information about chromatin accessibility. Interpreting the functional significance of these data sets requires knowledge of which regulators are likely to bind these regions. This can be achieved by using information about TF-binding preferences, or motifs, to identify TF-binding events that are likely to be functional. Although different approaches exist to map motifs to DNA sequences, a systematic evaluation of these tools in plants is missing. Here, we compare four motif-mapping tools widely used in the Arabidopsis (Arabidopsis thaliana) research community and evaluate their performance using chromatin immunoprecipitation data sets for 40 TFs. Downstream gene regulatory network (GRN) reconstruction was found to be sensitive to the motif mapper used. We further show that the low recall of Find Individual Motif Occurrences, one of the most frequently used motif-mapping tools, can be overcome by using an Ensemble approach, which combines results from different mapping tools. Several examples are provided demonstrating how the Ensemble approach extends our view on transcriptional control for TFs active in different biological processes. Finally, a protocol is presented to effectively derive more complete cell type-specific GRNs through the integrative analysis of open chromatin regions, known binding site information, and expression data sets. This approach will pave the way to increase our understanding of GRNs in different cellular conditions
Exploring Task Mappings on Heterogeneous MPSoCs using a Bias-Elitist Genetic Algorithm
Exploration of task mappings plays a crucial role in achieving high
performance in heterogeneous multi-processor system-on-chip (MPSoC) platforms.
The problem of optimally mapping a set of tasks onto a set of given
heterogeneous processors for maximal throughput has been known, in general, to
be NP-complete. The problem is further exacerbated when multiple applications
(i.e., bigger task sets) and the communication between tasks are also
considered. Previous research has shown that Genetic Algorithms (GA) typically
are a good choice to solve this problem when the solution space is relatively
small. However, when the size of the problem space increases, classic genetic
algorithms still suffer from the problem of long evolution times. To address
this problem, this paper proposes a novel bias-elitist genetic algorithm that
is guided by domain-specific heuristics to speed up the evolution process.
Experimental results reveal that our proposed algorithm is able to handle large
scale task mapping problems and produces high-quality mapping solutions in only
a short time period.Comment: 9 pages, 11 figures, uses algorithm2e.st
"Going back to our roots": second generation biocomputing
Researchers in the field of biocomputing have, for many years, successfully
"harvested and exploited" the natural world for inspiration in developing
systems that are robust, adaptable and capable of generating novel and even
"creative" solutions to human-defined problems. However, in this position paper
we argue that the time has now come for a reassessment of how we exploit
biology to generate new computational systems. Previous solutions (the "first
generation" of biocomputing techniques), whilst reasonably effective, are crude
analogues of actual biological systems. We believe that a new, inherently
inter-disciplinary approach is needed for the development of the emerging
"second generation" of bio-inspired methods. This new modus operandi will
require much closer interaction between the engineering and life sciences
communities, as well as a bidirectional flow of concepts, applications and
expertise. We support our argument by examining, in this new light, three
existing areas of biocomputing (genetic programming, artificial immune systems
and evolvable hardware), as well as an emerging area (natural genetic
engineering) which may provide useful pointers as to the way forward.Comment: Submitted to the International Journal of Unconventional Computin
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