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TCBB
2011
10 years 8 months ago
Comparison of Galled Trees
Galled trees, directed acyclic graphs that model evolutionary histories with isolated hybridization events, have become very popular due to both their biological significance and ...
Gabriel Cardona, Mercè Llabrés, Fran...
TCBB
2011
10 years 8 months ago
Ensemble Learning with Active Example Selection for Imbalanced Biomedical Data Classification
—In biomedical data, the imbalanced data problem occurs frequently and causes poor prediction performance for minority classes. It is because the trained classifiers are mostly d...
Sangyoon Oh, Min Su Lee, Byoung-Tak Zhang
TCBB
2011
10 years 8 months ago
Visual Exploration across Biomedical Databases
Abstract—Though biomedical research often draws on knowledge from a wide variety of fields, few visualization methods for biomedical data incorporate meaningful cross-database e...
Michael D. Lieberman, Sima Taheri, Huimin Guo, Fat...
TCBB
2011
10 years 8 months ago
Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays
— Probe defects are a major source of noise in gene expression studies. While existing approaches detect noisy probes based on external information such as genomic alignments, we...
Leo Lahti, Laura Elo, Tero Aittokallio, Samuel Kas...
TCBB
2011
10 years 8 months ago
Semi-Markov Models for Brownian Dynamics Permeation in Biological Ion Channels
—Constructing accurate computational models that explain how ions permeate through a biological ion channel is an important problem in biophysics and drug design. Brownian dynami...
Vikram Krishnamurthy, Kai Yiu Luk
TCBB
2011
10 years 8 months ago
A Partial Set Covering Model for Protein Mixture Identification Using Mass Spectrometry Data
—Protein identification is a key and essential step in mass spectrometry (MS) based proteome research. To date, there are many protein identification strategies that employ eithe...
Zengyou He, Can Yang, Weichuan Yu
TCBB
2011
10 years 8 months ago
Information-Theoretic Model of Evolution over Protein Communication Channel
—In this paper, we propose a communication model of evolution and investigate its information-theoretic bounds. The process of evolution is modeled as the retransmission of infor...
Liuling Gong, Nidhal Bouaynaya, Dan Schonfeld
TCBB
2011
10 years 8 months ago
Semantics and Ambiguity of Stochastic RNA Family Models
Stochastic models such as hidden Markov models or stochastic context free grammars can fail to return the correct, maximum likelihood solution in the case of semantic ambiguity. T...
Robert Giegerich, Christian Höner zu Siederdi...
TCBB
2011
10 years 8 months ago
Learning Genetic Regulatory Network Connectivity from Time Series Data
Recent experimental advances facilitate the collection of time series data that indicate which genes in a cell are expressed. This paper proposes an efficient method to generate th...
Nathan A. Barker, Chris J. Myers, Hiroyuki Kuwahar...
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