Grasping frequent subgraph mining for bioinformatics applications
Searching for interesting common subgraphs in graph data is a well-studied problem in data mining. Subgraph mining techniques focus on the discovery of patterns in graphs that exhibit a specific network struct... (Source: BioData Mining)
Source: BioData Mining - September 3, 2018 Category: Bioinformatics Authors: Aida Mrzic, Pieter Meysman, Wout Bittremieux, Pieter Moris, Boris Cule, Bart Goethals and Kris Laukens Tags: Review Source Type: research
Functional relevance for central cornea thickness-associated genetic variants by using integrative analyses
The genetic architecture underlying central cornea thickness (CCT) is far from understood. Most of the CCT-associated variants are located in the non-coding regions, raising the difficulty of following functio... (Source: BioData Mining)
Source: BioData Mining - August 15, 2018 Category: Bioinformatics Authors: Jing Zhang, Dan Wu, Yiqin Dai and Jianjiang Xu Tags: Research Source Type: research
Evolutionary methods for variable selection in the epidemiological modeling of cardiovascular diseases
This study implements an advanced evo... (Source: BioData Mining)
Source: BioData Mining - August 14, 2018 Category: Bioinformatics Authors: Christina Brester, Jussi Kauhanen, Tomi-Pekka Tuomainen, Sari Voutilainen, Mauno R önkkö, Kimmo Ronkainen, Eugene Semenkin and Mikko Kolehmainen Tags: Research Source Type: research
Protein folding prediction in the HP model using ions motion optimization with a greedy algorithm
The function of a protein is determined by its native protein structure. Among many protein prediction methods, the Hydrophobic-Polar (HP) model, an ab initio method, simplifies the protein folding prediction ... (Source: BioData Mining)
Source: BioData Mining - August 8, 2018 Category: Bioinformatics Authors: Cheng-Hong Yang, Kuo-Chuan Wu, Yu-Shiun Lin, Li-Yeh Chuang and Hsueh-Wei Chang Tags: Methodology Source Type: research
A multi-objective gene clustering algorithm guided by apriori biological knowledge with intensification and diversification strategies
Biologists aim to understand the genetic background of diseases, metabolic disorders or any other genetic condition. Microarrays are one of the main high-throughput technologies for collecting information abou... (Source: BioData Mining)
Source: BioData Mining - August 7, 2018 Category: Bioinformatics Authors: Jorge Parraga-Alava, Marcio Dorn and Mario Inostroza-Ponta Tags: Methodology Source Type: research
TRIQ: a new method to evaluate triclusters
Triclustering has shown to be a valuable tool for the analysis of microarray data since its appearance as an improvement of classical clustering and biclustering techniques. The standard for validation of tric... (Source: BioData Mining)
Source: BioData Mining - August 6, 2018 Category: Bioinformatics Authors: David Guti érrez-Avilés, Raúl Giráldez, Francisco Javier Gil-Cumbreras and Cristina Rubio-Escudero Tags: Research Source Type: research
PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia
Investigators often interpret genome-wide data by analyzing the expression levels of genes within pathways. While this within-pathway analysis is routine, the products of any one pathway can affect the activit... (Source: BioData Mining)
Source: BioData Mining - July 3, 2018 Category: Bioinformatics Authors: Kathleen M. Chen, Jie Tan, Gregory P. Way, Georgia Doing, Deborah A. Hogan and Casey S. Greene Tags: Software article Source Type: research
Integrative analysis of gene expression and methylation data for breast cancer cell lines
The deadly costs of cancer and necessity for an accurate method of early cancer detection have demanded the identification of genetic and epigenetic factors associated with cancer. DNA methylation, an epigenet... (Source: BioData Mining)
Source: BioData Mining - June 25, 2018 Category: Bioinformatics Authors: Catherine Li, Juyon Lee, Jessica Ding and Shuying Sun Tags: Research Source Type: research
Measuring associations between the microbiota and repeated measures of continuous clinical variables using a lasso-penalized generalized linear mixed model
Human microbiome studies in clinical settings generally focus on distinguishing the microbiota in health from that in disease at a specific point in time. However, microbiome samples may be associated with dis... (Source: BioData Mining)
Source: BioData Mining - June 15, 2018 Category: Bioinformatics Authors: Laura Tipton, Karen T. Cuenco, Laurence Huang, Ruth M. Greenblatt, Eric Kleerup, Frank Sciurba, Steven R. Duncan, Michael P. Donahoe, Alison Morris and Elodie Ghedin Tags: Research Source Type: research
Soft document clustering using a novel graph covering approach
In text mining, document clustering describes the efforts to assign unstructured documents to clusters, which in turn usually refer to topics. Clustering is widely used in science for data retrieval and organi... (Source: BioData Mining)
Source: BioData Mining - June 14, 2018 Category: Bioinformatics Authors: Jens D örpinghaus, Sebastian Schaaf and Marc Jacobs Tags: Methodology Source Type: research
Characterizing the effects of missing data and evaluating imputation methods for chemical prioritization applications using ToxPi
The Toxicological Priority Index (ToxPi) is a method for prioritization and profiling of chemicals that integrates data from diverse sources. However, individual data sources ( “assays”), such as in vitro bioas... (Source: BioData Mining)
Source: BioData Mining - June 13, 2018 Category: Bioinformatics Authors: Kimberly T. To, Rebecca C. Fry and David M. Reif Tags: Research Source Type: research
Feature selection for gene prediction in metagenomic fragments
Computational approaches, specifically machine-learning techniques, play an important role in many metagenomic analysis algorithms, such as gene prediction. Due to the large feature space, current de novo gene... (Source: BioData Mining)
Source: BioData Mining - June 7, 2018 Category: Bioinformatics Authors: Amani Al-Ajlan and Achraf El Allali Tags: Methodology Source Type: research
Connecting genetics and gene expression data for target prioritisation and drug repositioning
Developing new drugs continues to be a highly inefficient and costly business. By repurposing an existing compound for a different indication, drug repositioning offers an attractive alternative to traditional... (Source: BioData Mining)
Source: BioData Mining - May 31, 2018 Category: Bioinformatics Authors: Enrico Ferrero and Pankaj Agarwal Tags: Short report Source Type: research
Gene set analysis methods: a systematic comparison
Gene set analysis is a valuable tool to summarize high-dimensional gene expression data in terms of biologically relevant sets. This is an active area of research and numerous gene set analysis methods have be... (Source: BioData Mining)
Source: BioData Mining - May 31, 2018 Category: Bioinformatics Authors: Ravi Mathur, Daniel Rotroff, Jun Ma, Ali Shojaie and Alison Motsinger-Reif Tags: Research Source Type: research
Collective feature selection to identify crucial epistatic variants
Machine learning methods have gained popularity and practicality in identifying linear and non-linear effects of variants associated with complex disease/traits. Detection of epistatic interactions still remai... (Source: BioData Mining)
Source: BioData Mining - April 19, 2018 Category: Bioinformatics Authors: Shefali S. Verma, Anastasia Lucas, Xinyuan Zhang, Yogasudha Veturi, Scott Dudek, Binglan Li, Ruowang Li, Ryan Urbanowicz, Jason H. Moore, Dokyoon Kim and Marylyn D. Ritchie Tags: Research Source Type: research
