Volume 7 Supplement 7

Proceedings of the Great Lakes Bioinformatics Conference 2013

Proceedings

Edited by Victor Jin

Publication of this supplement has not been supported by sponsorship. Information about the source of funding for publication charges can be found in the individual articles. Articles have undergone the journal's standard review process for supplements. The Supplement Editor declares that he has no competing interests.

Great Lakes Bioinformatics Conference 2013. Go to conference site.

Pittsburgh, PA, USA14-16 May 2013

The impact of structural diversity and parameterization on maps of the protein universe

Low dimensional maps of protein structure space (MPSS) provide a powerful global representation of all proteins. In such mappings structural relationships are depicted through spatial adjacency of points, each...

Authors: Daniel Asarnow and Rahul Singh

Citation: BMC Proceedings 2013 7(Suppl 7):S1

Content type: Proceedings Published on: 20 December 2013
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Conceptualization of molecular findings by mining gene annotations

The Gene Ontology (GO) is an ontology representing molecular biology concepts related to genes and their products. Current annotations from the GO Consortium tend to be highly specific, and contemporary genome...

Authors: Vicky Chen and Xinghua Lu

Citation: BMC Proceedings 2013 7(Suppl 7):S2

Content type: Proceedings Published on: 20 December 2013
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A new approach to enhance the performance of decision tree for classifying gene expression data

Gene expression data classification is a challenging task due to the large dimensionality and very small number of samples. Decision tree is one of the popular machine learning approaches to address such class...

Authors: Md Rafiul Hassan and Ramamohanarao Kotagiri

Citation: BMC Proceedings 2013 7(Suppl 7):S3

Content type: Proceedings Published on: 20 December 2013
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Better primer design for metagenomics applications by increasing taxonomic distinguishability

Current methods of understanding microbiome composition and structure rely on accurately estimating the number of distinct species and their relative abundance. Most of these methods require an efficient PCR w...

Authors: Melita Jaric, Jonathan Segal, Eugenia Silva-Herzog, Lisa Schneper, Kalai Mathee and Giri Narasimhan

Citation: BMC Proceedings 2013 7(Suppl 7):S4

Content type: Proceedings Published on: 20 December 2013
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Multi-task feature selection in microarray data by binary integer programming

A major challenge in microarray classification is that the number of features is typically orders of magnitude larger than the number of examples. In this paper, we propose a novel feature filter algorithm to ...

Authors: Liang Lan and Slobodan Vucetic

Citation: BMC Proceedings 2013 7(Suppl 7):S5

Content type: Proceedings Published on: 20 December 2013
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Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods

Elucidation of protein-protein interaction (PPI) networks is important for understanding disease mechanisms and for drug discovery. Tertiary-structure-based in silico PPI prediction methods have been developed wi...

Authors: Masahito Ohue, Yuri Matsuzaki, Takehiro Shimoda, Takashi Ishida and Yutaka Akiyama

Citation: BMC Proceedings 2013 7(Suppl 7):S6

Content type: Proceedings Published on: 20 December 2013
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Adaptive bandwidth kernel density estimation for next-generation sequencing data

High-throughput sequencing experiments can be viewed as measuring some sort of a "genomic signal" that may represent a biological event such as the binding of a transcription factor to the genome, locations of...

Authors: Parameswaran Ramachandran and Theodore J Perkins

Citation: BMC Proceedings 2013 7(Suppl 7):S7

Content type: Proceedings Published on: 20 December 2013
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MicroRNA identification using linear dimensionality reduction with explicit feature mapping

microRNAs are a class of small RNAs, about 20 nt long, which regulate cellular processes in animals and plants. Identifying microRNAs is one of the most important tasks in gene regulation studies. The main fea...

Authors: Navid Shakiba and Luis Rueda

Citation: BMC Proceedings 2013 7(Suppl 7):S8

Content type: Proceedings Published on: 20 December 2013
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BiCluE - Exact and heuristic algorithms for weighted bi-cluster editing of biomedical data

The explosion of biological data has dramatically reformed today's biology research. The biggest challenge to biologists and bioinformaticians is the integration and analysis of large quantity of data to provi...

Authors: Peng Sun, Jiong Guo and Jan Baumbach

Citation: BMC Proceedings 2013 7(Suppl 7):S9

Content type: Proceedings Published on: 20 December 2013
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A neural network approach to multi-biomarker panel discovery by high-throughput plasma proteomics profiling of breast cancer

In the past several years, there has been increasing interest and enthusiasm in molecular biomarkers as tools for early detection of cancer. Liquid chromatography tandem mass spectrometry (LC/MS/MS) based plas...

Authors: Fan Zhang, Jake Chen, Mu Wang and Renee Drabier

Citation: BMC Proceedings 2013 7(Suppl 7):S10

Content type: Proceedings Published on: 20 December 2013
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Building a web-based tool to support clinical decisions in the control of Chlamydia trachomatis and Neisseria gonorrhoeae infections

Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) are the agents of two common, sexually transmitted diseases afflicting women in the United States (

Authors: Kun Zhao, Fasheng Qiu and Guantao Chen

Citation: BMC Proceedings 2013 7(Suppl 7):S11

Content type: Proceedings Published on: 20 December 2013
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Proceedings of the Great Lakes Bioinformatics Conference 2013

Proceedings

The impact of structural diversity and parameterization on maps of the protein universe

Conceptualization of molecular findings by mining gene annotations

A new approach to enhance the performance of decision tree for classifying gene expression data

Better primer design for metagenomics applications by increasing taxonomic distinguishability

Multi-task feature selection in microarray data by binary integer programming

Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods

Adaptive bandwidth kernel density estimation for next-generation sequencing data

MicroRNA identification using linear dimensionality reduction with explicit feature mapping

BiCluE - Exact and heuristic algorithms for weighted bi-cluster editing of biomedical data

A neural network approach to multi-biomarker panel discovery by high-throughput plasma proteomics profiling of breast cancer

Building a web-based tool to support clinical decisions in the control of Chlamydia trachomatis and Neisseria gonorrhoeae infections

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