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Article
Open AccessMultiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C
Technology for measuring 3D genome topology is increasingly important for studying gene regulation, for genome assembly and for map** of genome rearrangements. Hi-C and other ligation-based methods have beco...
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Protocol
Bioinformatic Identification of Plant Hydroxyproline-Rich Glycoproteins
Hydroxyproline-rich glycoproteins (HRGPs) are a superfamily of plant cell wall proteins that function in diverse aspects of plant growth and development. This superfamily consists of three members: arabinogala...
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Article
Open AccessBioinformatic Identification and Analysis of Hydroxyproline-Rich Glycoproteins in Populus trichocarpa
Hydroxyproline-rich glycoproteins (HRGPs) constitute a plant cell wall protein superfamily that functions in diverse aspects of growth and development. This superfamily contains three members: the highly glyco...
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Article
Open AccessWordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures
An important focus of genomic science is the discovery and characterization of all functional elements within genomes. In silico methods are used in genome studies to discover putative regulatory genomic elements...
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Article
Open AccessThe word landscape of the non-coding segments of the Arabidopsis thaliana genome
Genome sequences can be conceptualized as arrangements of motifs or words. The frequencies and positional distributions of these words within particular non-coding genomic segments provide important insights i...
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Article
Open AccessWord-based characterization of promoters involved in human DNA repair pathways
DNA repair genes provide an important contribution towards the surveillance and repair of DNA damage. These genes produce a large network of interacting proteins whose mRNA expression is likely to be regulated...
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Article
Adaptive resource management for dynamic distributed real-time applications
The dynamic distributed real-time applications run on clusters with varying execution time, so re-allocation of resources is critical to meet the applications’s deadline. In this paper we present two adaptive ...
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Chapter and Conference Paper
Real-Time Performance Estimation for Dynamic, Distributed Real-Time Systems
The main contribution of this paper is accurate analysis of real-time performance for dynamic real-time applications. A wrong system performance analysis can lead to a catastrophe in a dynamic real-time system...
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Article
Load balancing for dynamic real-time systems
Some classes of real-time systems function in environments, which cannot be modeled with static approaches. In such environments, the arrival rates of events which drive transient computations may be unknown. ...
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Chapter and Conference Paper
Quality of Service Negotiation for Distributed, Dynamic Real-time Systems
Dynamic, distributed, real-time systems control an environment that varies widely without any time-invariant statistical or deterministic characteristic, are spread across multiple loosely-coupled computers, a...
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Chapter and Conference Paper
5th International Workshop on Embedded/Distributed HPC Systems and Applications (EHPC 2000)
The International Workshop on Embedded/Distributed HPC Systems and Applications (EHPC) is a forum for the presentation and discussion of approaches, research findings, and experiences in the applications of Hi...
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Chapter and Conference Paper
Network Load Monitoring in Distributed Systems
Monitoring the performance of a network by which a real-time distributed system is connected is very important. If the system is adaptive or dynamic, the resource manager can use this information to create or ...
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Chapter and Conference Paper
A distributed system reference architecture for adaptive QoS and resource management
This paper deals with large, distributed real-time systems that have execution times and resource utilizations which cannot be characterized a priori. (The motivation for our work is provided in part by the chara...
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Article
Editorial
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Chapter and Conference Paper
A resource management model for dynamic, scalable, dependable, real-time systems
Dynamic real-time systems function in unpredictable environments and have requirements that span many domains such as time, survivability, and scalability. The system requirements are typically determined as a...
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Article
Metrics for quality and concurrency in object-based systems
This paper defines metrics for object-based systems. A hierarchical, abstract representation of object-based software is presented, and is used to define programming-language-independent metrics formulas. Nove...
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Article
Metrics for assessment of designs and implementations during reengineering of computer-based systems
Modern computer-based systems have many required characteristics, including performance, concurrency, timeliness, availability, dependability, safety and security. Aging computer-based systems are being reengi...
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Article
A model for scheduling of object-based, distributed real-time systems
This paper describes a general model for pre-run-time scheduling of distributed real-time systems that are composed of abstract data types (definable in languages such as Ada, Clu and Modula-2) and abstract da...
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Chapter and Conference Paper
Formal Methods and Algorithms for Parallel Real-Time Computing
Parallel computers are becoming increasingly popular as vehicles for speeding up the execution of programs, enabling more real-time processes to execute and to meet deadlines than would be possible otherwise. ...
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Chapter and Conference Paper
Techniques for Complex Systems Development
In the Real-Time Computing Laboratory at NJIT, we are studying the techniques of vertical integration and automatic synthesis in the context of complex systems1.
