Characterizing human genomic coevolution in locus-gene regulatory interactions
Coevolution has been used to identify and predict interactions and functional relationships between proteins of many different organisms including humans. Current efforts in annotating the human genome increas... (Source: BioData Mining)
Source: BioData Mining - March 15, 2019 Category: Bioinformatics Authors: Daniel Savel and Mehmet Koyut ürk Tags: Research Source Type: research
Encodings and models for antimicrobial peptide classification for multi-resistant pathogens
Antimicrobial peptides (AMPs) are part of the inherent immune system. In fact, they occur in almost all organisms including, e.g., plants, animals, and humans. Remarkably, they show effectivity also against mu... (Source: BioData Mining)
Source: BioData Mining - March 4, 2019 Category: Bioinformatics Authors: Sebastian Sp änig and Dominik Heider Tags: Review Source Type: research
Testing the assumptions of parametric linear models: the need for biological data mining in disciplines such as human genetics
(Source: BioData Mining)
Source: BioData Mining - February 11, 2019 Category: Bioinformatics Authors: Jason H. Moore, Trudy F. C. Mackay and Scott M. Williams Tags: Editorial Source Type: research
Approximate kernel reconstruction for time-varying networks
Most existing algorithms for modeling and analyzing molecular networks assume a static or time-invariant network topology. Such view, however, does not render the temporal evolution of the underlying biologica... (Source: BioData Mining)
Source: BioData Mining - February 6, 2019 Category: Bioinformatics Authors: Gregory Ditzler, Nidhal Bouaynaya, Roman Shterenberg and Hassan M. Fathallah-Shaykh Tags: Research Source Type: research
A biplot correlation range for group-wise metabolite selection in mass spectrometry
Analytic methods are available to acquire extensive metabolic information in a cost-effective manner for personalized medicine, yet disease risk and diagnosis mostly rely upon individual biomarkers based on st... (Source: BioData Mining)
Source: BioData Mining - February 4, 2019 Category: Bioinformatics Authors: Youngja H Park, Taewoon Kong, James R. Roede, Dean P. Jones and Kichun Lee Tags: Research Source Type: research
Predicting opioid dependence from electronic health records with machine learning
The opioid epidemic in the United States is averaging over 100 deaths per day due to overdose. The effectiveness of opioids as pain treatments, and the drug-seeking behavior of opioid addicts, leads physicians... (Source: BioData Mining)
Source: BioData Mining - January 29, 2019 Category: Bioinformatics Authors: Randall J. Ellis, Zichen Wang, Nicholas Genes and Avi Ma ’ayan Tags: Research Source Type: research
Use case driven evaluation of open databases for pediatric cancer research
A plethora of Web resources are available offering information on clinical, pre-clinical, genomic and theoretical aspects of cancer, including not only the comprehensive cancer projects as ICGC and TCGA, but a... (Source: BioData Mining)
Source: BioData Mining - January 15, 2019 Category: Bioinformatics Authors: Fleur Jeanquartier, Claire Jean-Quartier and Andreas Holzinger Tags: Research Source Type: research
Application of an interpretable classification model on Early Folding Residues during protein folding
Machine learning strategies are prominent tools for data analysis. Especially in life sciences, they have become increasingly important to handle the growing datasets collected by the scientific community. Mea... (Source: BioData Mining)
Source: BioData Mining - January 5, 2019 Category: Bioinformatics Authors: Sebastian Bittrich, Marika Kaden, Christoph Leberecht, Florian Kaiser, Thomas Villmann and Dirk Labudde Tags: Methodology Source Type: research
Unified Cox model based multifactor dimensionality reduction method for gene-gene interaction analysis of the survival phenotype
One strategy for addressing missing heritability in genome-wide association study is gene-gene interaction analysis, which, unlike a single gene approach, involves high-dimensionality. The multifactor dimensio... (Source: BioData Mining)
Source: BioData Mining - December 14, 2018 Category: Bioinformatics Authors: Seungyeoun Lee, Donghee Son, Yongkang Kim, Wenbao Yu and Taesung Park Tags: Methodology Source Type: research
Distributed retrieval engine for the development of cloud-deployed biological databases
The integration of cloud resources with federated data retrieval has the potential of improving the maintenance, accessibility and performance of specialized databases in the biomedical field. However, such an... (Source: BioData Mining)
Source: BioData Mining - November 12, 2018 Category: Bioinformatics Authors: David Bouzaglo, Israel Chasida and Elishai Ezra Tsur Tags: Software article Source Type: research
Knomics-Biota - a system for exploratory analysis of human gut microbiota data
Metagenomic surveys of human microbiota are becoming increasingly widespread in academic research as well as in food and pharmaceutical industries and clinical context. Intuitive tools for investigating experi... (Source: BioData Mining)
Source: BioData Mining - November 6, 2018 Category: Bioinformatics Authors: Daria Efimova, Alexander Tyakht, Anna Popenko, Anatoly Vasilyev, Ilya Altukhov, Nikita Dovidchenko, Vera Odintsova, Natalya Klimenko, Robert Loshkarev, Maria Pashkova, Anna Elizarova, Viktoriya Voroshilova, Sergei Slavskii, Yury Pekov, Ekaterina Filippova Tags: Software article Source Type: research
A fast forward 3D connection algorithm for mitochondria and synapse segmentations from serial EM images
It is becoming increasingly clear that the quantification of mitochondria and synapses is of great significance to understand the function of biological nervous systems. Electron microscopy (EM), with the nece... (Source: BioData Mining)
Source: BioData Mining - November 5, 2018 Category: Bioinformatics Authors: Weifu Li, Jing Liu, Chi Xiao, Hao Deng, Qiwei Xie and Hua Han Tags: Methodology Source Type: research
Transition-transversion encoding and genetic relationship metric in ReliefF feature selection improves pathway enrichment in GWAS
ReliefF is a nearest-neighbor based feature selection algorithm that efficiently detects variants that are important due to statistical interactions or epistasis. For categorical predictors, like genotypes, th... (Source: BioData Mining)
Source: BioData Mining - November 3, 2018 Category: Bioinformatics Authors: M. Arabnejad, B. A. Dawkins, W. S. Bush, B. C. White, A. R. Harkness and B. A. McKinney Tags: Methodology Source Type: research
Combining DNA methylation and RNA sequencing data of cancer for supervised knowledge extraction
In the Next Generation Sequencing (NGS) era a large amount of biological data is being sequenced, analyzed, and stored in many public databases, whose interoperability is often required to allow an enhanced ac... (Source: BioData Mining)
Source: BioData Mining - October 25, 2018 Category: Bioinformatics Authors: Eleonora Cappelli, Giovanni Felici and Emanuel Weitschek Tags: Methodology Source Type: research
To know the objective is not (necessarily) to know the objective function
(Source: BioData Mining)
Source: BioData Mining - October 4, 2018 Category: Bioinformatics Authors: Moshe Sipper, Ryan J. Urbanowicz and Jason H. Moore Tags: Editorial Source Type: research
