A Multi-Fold String Kernel for Sequence Classification

Maiti, Aniruddha ;   Ghorai, Santanu ;   Mukherjee, Anirban

Tags Algorithms and computational tools for proteomicsBiomedical data-driven modelingAnalysis of high-throughput systems biology data

A novel framework is proposed to classify biological sequences using a kernel. It considers the topological information along with the primary...

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An Optimal Method to Segment Piecewise Poisson Distributed Signals with Application to Sequencing Data

Duan, Junbo ;   Soussen, Charles ;   Brie, David ;   IDIER, Jérôme ;   Wang, Yu-Ping ;   Wan, Mingxi

Tags Analysis of high-throughput systems biology dataAlgorithms and techniques for systems modelingInverse problems in biology

To analyze the next generation sequencing data, the so-called read depth signal is often segmented with standard segmentation tools....

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C. Elegans Locomotion Analysis using Algorithmic Information Theory

Skandari, Roghieh ;   Le Bihan, Nicolas ;   Manton, Jonathan

Tags Advances in theory of biological networksAlgorithms and computational tools for proteomicsAnalysis of high-throughput systems biology data

This article investigates the use of algorithmic information theory to analyse C. elegans datasets. The ability of complexity measures to...

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DNA Assembly with De Bruijn Graphs on FPGA

Poirier, Carl ;   Gosselin, Benoit ;   Fortier, Paul

Tags Analysis of high-throughput systems biology data

This project aims to see if accelerators based on FPGAs are worthwhile for DNA assembly. It involves reprogramming an already existing...

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Effect of Low-Expression Gene Filtering on Detection of Differentially Expressed Genes in RNA-Seq Data

Sha, Ying ;   Phan, John H. ;   Wang, May D.

Tags Analysis of high-throughput systems biology dataBiomedical data-driven modeling

We compare methods for filtering RNA-seq low-expression genes and investigate the effect of filtering on detection of differentially...

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Genome-Based Microorganism Classification using Coalition Formulation Game

Chung, Byung Chang ;   Han, Gyu-Bum ;   Cho, Dong-Ho

Tags Algorithms and techniques for systems modelingAnalysis of high-throughput systems biology dataBiomedical data-driven modeling

Genome-based microorganism classification is the one of interesting issues in microorganism taxonomy. However, the advance in sequencing...

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Metabolite Analysis in Sepsis through Conditional Independence Maps

Ribas Ripoll, Vicent J. ;   Romay, Eduardo ;   Brunelli, Laura ;   Pastorelli, Roberta ;   Goma, Gemma ;   Navas, Ana ;   Ferrer, Ricard ;   Artigas, Antoni

Tags Analysis of high-throughput systems biology dataBiomedical data-driven modelingMining clinical data

Sepsis is a transversal pathology and one of the main causes of death at the Intensive Care Unit (ICU). It has in fact become the tenth...

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Performance Comparison of Next Generation Sequencing Platforms

Ergüner, Bekir ;   Sa??ro?lu, Mahmut ?amil ;   Üstek, Duran

Tags Analysis of high-throughput systems biology data

Next Generation DNA Sequencing technologies offer ultra high sequencing throughput for very low prices. The increase in throughput and...

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SRIdent: A Novel Pipeline for Real-Time Identification of Species from High-throughput Sequencing Reads in Metagenomics and Clinical Diagnostic Assays

Karimi, Ramin ;   Hajdu, Andras

Tags Analysis of high-throughput systems biology dataAdvances in theory of biological networksMedical decision making

New advances in rapid sequencing of large amounts of DNA have brought a great potential for the study of complex communities of...

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Tracking Single-Cells in Overcrowded Bacterial Colonies

Balomenos, Athanasios ;   Tsakanikas, Panagiotis ;   Manoloakos, Elias

Tags Analysis of high-throughput systems biology dataStructured data visualization

Cell tracking enables data extraction from time-lapse "cell movies" and promotes modeling biological processes at the single-cell...

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