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WABI
2010
Springer
177views Bioinformatics» more  WABI 2010»
9 years 6 months ago
Estimation of Alternative Splicing isoform Frequencies from RNA-Seq Data
In this paper we present a novel expectation-maximization algorithm for inference of alternative splicing isoform frequencies from high-throughput transcriptome sequencing (RNA-Seq...
Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Al...
WABI
2010
Springer
124views Bioinformatics» more  WABI 2010»
9 years 6 months ago
Improved Orientations of Physical Networks
Abstract. The orientation of physical networks is a prime task in deciphering the signaling-regulatory circuitry of the cell. One manifestation of this computational task is as a m...
Iftah Gamzu, Danny Segev, Roded Sharan
WABI
2010
Springer
128views Bioinformatics» more  WABI 2010»
9 years 6 months ago
Sparsification of RNA Structure Prediction Including Pseudoknots
Background: Although many RNA molecules contain pseudoknots, computational prediction of pseudoknotted RNA structure is still in its infancy due to high running time and space con...
Mathias Möhl, Raheleh Salari, Sebastian Will,...
WABI
2010
Springer
143views Bioinformatics» more  WABI 2010»
9 years 6 months ago
Swiftly Computing Center Strings
The center string (or closest string) problem is a classical computer science problem with important applications in computational biology. Given k input strings and a distance thr...
Franziska Hufsky, Léon Kuchenbecker, Kathar...
WABI
2010
Springer
167views Bioinformatics» more  WABI 2010»
9 years 6 months ago
Quantifying the Strength of Natural Selection of a Motif Sequence
Quantification of selective pressures on regulatory sequences is a central question in studying the evolution of gene regulatory networks. Previous methods focus primarily on sing...
Chen-Hsiang Yeang
WABI
2010
Springer
172views Bioinformatics» more  WABI 2010»
9 years 6 months ago
Fast Mapping and Precise Alignment of AB SOLiD Color Reads to Reference DNA
Abstract. Applied Biosystems’ SOLiD system offers a low-cost alternative to the traditional Sanger method of DNA sequencing. We introduce two main algorithms of mapping SOLiD’...
Miklós Csürös, Szilveszter Juhos,...
PRIB
2010
Springer
123views Bioinformatics» more  PRIB 2010»
9 years 6 months ago
Machine Learning Study of DNA Binding by Transcription Factors from the LacI Family
We studied 1372 LacI-family transcription factors and their 4484 DNA binding sites using machine learning algorithms and feature selection techniques. The Naive Bayes classifier a...
Gennady G. Fedonin, Mikhail S. Gelfand
PRIB
2010
Springer
242views Bioinformatics» more  PRIB 2010»
9 years 6 months ago
Consensus of Ambiguity: Theory and Application of Active Learning for Biomedical Image Analysis
Abstract. Supervised classifiers require manually labeled training samples to classify unlabeled objects. Active Learning (AL) can be used to selectively label only “ambiguous...
Scott Doyle, Anant Madabhushi
PRIB
2010
Springer
192views Bioinformatics» more  PRIB 2010»
9 years 6 months ago
Structured Output Prediction of Anti-cancer Drug Activity
We present a structured output prediction approach for classifying potential anti-cancer drugs. Our QSAR model takes as input a description of a molecule and predicts the activity...
Hongyu Su, Markus Heinonen, Juho Rousu
JBI
2010
127views Bioinformatics» more  JBI 2010»
9 years 6 months ago
Using text to build semantic networks for pharmacogenomics
Adrien Coulet, Nigam H. Shah, Yael Garten, Mark A....
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