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BioData Mining

ISSN Print: 1756-0381

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Website: http://www.biodatamining.org

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Identification of new biomarker candidates for glucocorticoid induced insulin resistance using literature mining

Fleuren Wilco WM,Toonen Erik JM,Verhoeven Stefan,Frijters Raoul

Risk score modeling of multiple gene to gene interactions using aggregated-multifactor dimensionality reduction

Dai Hongying,Charnigo Richard J,Becker Mara L,Leeder J

Visually integrating and exploring high throughput Phenome-Wide Association Study (PheWAS) results using PheWAS-View

Sarah A Pendergrass, Scott Dudek, Dana C Crawford, Marylyn D Ritchie

Weighted multiple testing procedures for genomic studies

Jiang Gui, Tor D Tosteson, Mark Borsuk

‘MicroRNA Targets’, a new AthaMap web-tool for genome-wide identification of miRNA targets in Arabidopsis thaliana

Lorenz Bülow, Julio C. Bolívar, Jonas Ruhe, Yuri Brill, Reinhard Hehl

How do alignment programs perform on sequencing data with varying qualities and from repetitive regions?

Xiaoqing Yu, Kishore Guda, Joseph Willis, Martina Veigl, Zhenghe Wang, Sanford Markowitz, Mark Adams, Shuying Sun

Global tests of P-values for multifactor dimensionality reduction models in selection of optimal number of target genes

Hongying Dai, Madhusudan Bhandary, Mara L Becker, Steve J Leeder, Roger Gaedigk, Alison A Motsinger-Reif

A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization

Johannes Tuikkala, Heidi V？h？maa, Pekka Salmela, Olli S Nevalainen, Tero Aittokallio

Caipirini: using gene sets to rank literature

Theodoros G Soldatos, Seán I O'Donoghue, Venkata P Satagopam, Adriano Barbosa-Silva, Georgios A Pavlopoulos, Ana Wanderley-Nogueira, Nina Soares-Cavalcanti, Reinhard Schneider

Finding biomarkers in non-model species: literature mining of transcription factors involved in bovine embryo development

Turenne Nicolas,Tiys Evgeniy,Ivanisenko Vladimir,Yudin Nikolay

Application of a spatially-weighted Relief algorithm for ranking genetic predictors of disease

Stokes Matthew E,Visweswaran Shyam

Logic minimization and rule extraction for identification of functional sites in molecular sequences

Cruz-Cano Raul,Lee Mei-Ling,Leung Ming-Ying

Gene ontology analysis of pairwise genetic associations in two genome-wide studies of sporadic ALS

Kim Nora,Andrews Peter C,Asselbergs Folkert W,Frost H

Murine colon proteome and characterization of the protein pathways

Magdeldin Sameh,Yoshida Yutaka,Li Huiping,Maeda Yoshitaka

An automated framework for hypotheses generation using literature

Abedi Vida,Zand Ramin,Yeasin Mohammed,Faisal Fazle

Predicting the difficulty of pure, strict, epistatic models: metrics for simulated model selection

Urbanowicz Ryan J,Kiralis Jeff,Fisher Jonathan M,Moore Jason H

A comparison and evaluation of five biclustering algorithms by quantifying goodness of biclusters for gene expression data

Li Li,Guo Yang,Wu Wenwu,Shi Youyi

Molecular network analysis of human microRNA targetome: from cancers to Alzheimer’s disease

Satoh Jun-ichi

Peer2ref: a peer-reviewer finding web tool that uses author disambiguation

Andrade-Navarro Miguel A,Palidwor Gareth A,Perez-Iratxeta Carol

Evolving hard problems: Generating human genetics datasets with a complex etiology

Daniel S Himmelstein, Casey S Greene, Jason H Moore

Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data

Sami K Kilpinen, Kalle A Ojala, Olli P Kallioniemi

Detection of changes in gene regulatory patterns, elicited by perturbations of the Hsp90 molecular chaperone complex, by visualizing multiple experiments with an animation

Pablo C Echeverría, Fedor Forafonov, Deo P Pandey, Guillaume Mühlebach, Didier Picard

Mining beyond the exome

Davnah Urbach, Jason H Moore

Detection of putative new mutacins by bioinformatic analysis using available web tools

Guillaume G Nicolas

Blurring contact maps of thousands of proteins: what we can learn by reconstructing 3D structure

Marco Vassura, Pietro Di Lena, Luciano Margara, Maria Mirto, Giovanni Aloisio, Piero Fariselli, Rita Casadio

The spatial dimension in biological data mining

Davnah Urbach, Jason H Moore

Improved Bevirimat resistance prediction by combination of structural and sequence-based classifiers

J Nikolaj Dybowski, Mona Riemenschneider, Sascha Hauke, Martin Pyka, Jens Verheyen, Daniel Hoffmann, Dominik Heider

The effects of linkage disequilibrium in large scale SNP datasets for MDR

Benjamin J Grady, Eric S Torstenson, Marylyn D Ritchie

A comparison of machine learning techniques for survival prediction in breast cancer

Leonardo Vanneschi, Antonella Farinaccio, Giancarlo Mauri, Mauro Antoniotti, Paolo Provero, Mario Giacobini

Rule based classifier for the analysis of gene-gene and gene-environment interactions in genetic association studies

Thorsten Lehr, Jing Yuan, Dirk Zeumer, Supriya Jayadev, Marylyn D Ritchie

Preprocessing differential methylation hybridization microarray data

Shuying Sun, Yi-Wen Huang, Pearlly S Yan, Tim HM Huang, Shili Lin

Mining the diseasome

Davnah Urbach, Jason H Moore

Biclustering of Gene Expression Data by Correlation-Based Scatter Search

Juan A Nepomuceno, Alicia Troncoso, Jesús S Aguilar-Ruiz

An R package implementation of multifactor dimensionality reduction

Stacey J Winham, Alison A Motsinger-Reif

Taxon ordering in phylogenetic trees by means of evolutionary algorithms

Francesco Cerutti, Luigi Bertolotti, Tony L Goldberg, Mario Giacobini

DADA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization

Sinan Erten, Gurkan Bebek, Rob M Ewing, Mehmet Koyutürk

Using graph theory to analyze biological networks

Georgios A Pavlopoulos, Maria Secrier, Charalampos N Moschopoulos, Theodoros G Soldatos, Sophia Kossida, Jan Aerts, Reinhard Schneider, Pantelis G Bagos

Discrete derivative: a data slicing algorithm for exploration of sharing biological networks between rheumatoid arthritis and coronary heart disease

Guang Zheng, Miao Jiang, Xiaojuan He, Jing Zhao, Hongtao Guo, Gao Chen, Qinglin Zha, Aiping Lu

pGQL: A probabilistic graphical query language for gene expression time courses

Ruben Schilling, Ivan G Costa, Alexander Schliep

Hill-Climbing search and diversification within an evolutionary approach to protein structure prediction

Camelia Chira, Dragos Horvath, D Dumitrescu

A comparison of genomic copy number calls by Partek Genomics Suite, Genotyping Console and Birdsuite algorithms to quantitative PCR

Britney L Grayson, Thomas M Aune

Comprehensive analysis of human microRNA target networks

Jun-ichi Satoh, Hiroko Tabunoki

A Normalized Tree Index for identification of correlated clinical parameters in microarray experiments

Christian W Martin, Anika Tauchen, Anke Becker, Tim W Nattkemper

Interpol: An R package for preprocessing of protein sequences

Dominik Heider, Daniel Hoffmann

Data mining and the evolution of biological complexity

Davnah Urbach, Jason H Moore

Transcriptome bioinformatic analysis identifies potential therapeutic mechanism of pentylenetetrazole in down syndrome

Abhay Sharma

Grammatical evolution decision trees for detecting gene-gene interactions

Alison A Motsinger-Reif, Sushamna Deodhar, Stacey J Winham, Nicholas E Hardison

A reference guide for tree analysis and visualization

Georgios A Pavlopoulos, Theodoros G Soldatos, Adriano Barbosa-Silva, Reinhard Schneider

An extended data mining method for identifying differentially expressed assay-specific signatures in functional genomic studies

Derrick K Rollins, AiLing Teh

Synthesis-View: visualization and interpretation of SNP association results for multi-cohort, multi-phenotype data and meta-analysis

Sarah A Pendergrass, Scott M Dudek, Dana C Crawford, Marylyn D Ritchie

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